My own take on the evil god matter is it's an alignment/focus matter that determines if they can rank a formal church in a good or neutral community--generally, churches that can produce priests who will fit into the community will have them. Those that can't generally won't...
Let me give you a quick example, using the PHB gods...
HEXTOR will often have a church in an area. Many of these will be LN churches that attempt to sell him as a sort of uber-disciplined war god, while the others will be vile-tempered LE churches which basically demand that people pay Hextor tribute, or else... Relationships with other, more-hardline churches and priests of Hextor are going to depend on hierarchy and philosophy--for example, the Order of the Iron Fist is a largely LN organisation that sees itself as a monastic tradition training hard warriors to face a grim world. It does not get along with the LE Orthodox Church of Hextor, which is largely backed by the Empire of Asir, a gigantic, partially theocratic dictatorship. The Order sees the Church as giving into worldly politics and losing sight of Hextor's spiritual significance--the Church sees the Order as air-headed fools whose philosophing has obscured Hextor's practical message, which is of course, the Church of Hextor running the show. Still, they can manage an uneasy coexistance, while neither of them can get along with various NE cult leaders who, gathering followers together, proclaim themselves the 'Chosen of Hextor' and proceed to either cut a bloody swath through the land until some hero stops them, or plot in secret to unleash ancient evils/free devils/kick puppies, etc...
NERULL might have a LE church in the area, one that will claim to have given up all the human sacrifice and undead creation parts of the religion, and that is probably lying, though you won't catch them at it. It's quite possible that they have come to some formal relationship with the city government, allowing them to worship their grim god and yet still be functioning members of the community-- serving as executioners for criminals, to give an example. Most of their worship is in the form of 'Please Lord Nerull, don't kill my spouse', 'Oh, mighty Reaper, don't let my children come back as zombies', and the occasional, half-guilty 'Oh Lord of Bones--if Hew the Milner could drop dead--of natural causes, I'd be ever so thankful...' The church is probably willing to shelter less social members of the religion, as long as they don't start any trouble, and move out quickly. It should be pointed out that Nerull's cult has a rival in Wee Jas, and so they aren't always going to have a church.
VECNA will have LE or NE churches that attempt to set themselves up as information brokers, possessers of mystical secrets, and sellers of magical items. They also claim to have given up the human sacrifice and undeath stuff, and some of them might be telling the truth, because these guys are aiming at bigger game. Your local church of Vecna will try to put on a friendly front as they make themselves indispensable to the residents and government--and gather blackmail material. They are very likely to try to come to arrangement with the local criminal element, and meddle frequently in local politics. Naturally, the church is always in danger of being raided by the local authorities, forcibly disbanded or arrested, so they spend a lot of time greasing wheels, and making sure they have allies. They're perfectly willing to channel support to the more extreme members of the religion, but like the Nerullites, don't want them around sullying their home turf. And once again, rivalries and problems with the local authorities mean you're not always going to have a church.
ERYNTHUL usually does not have a local church, since his priesthood are basically serial killers. Usually, his faith is represented by secretive cult cells meeting in basements and sewers, and scheming to kill people. Erynthul is the sort of god that your more civilized sort doesn't like to talk about, or even give money to. I mean, the other evil gods have--some variety. Some ambivelance. Hextor is lord of Force, as well as Tyranny, Nerull is god of Death in general, not just Undead Things That Will Not Rest in the Earth, and Vecna's Secrets don't have to be Vile Secrets That Man Was Not Meant To Know. You can do your business with them and come out unsullied. Erynthul's God of Murder and Slaughter. You maybe toss out a quick prayer to him in fear and anger every once and while, but you don't worship him. It just leaves you feeling--dirty. It takes a special something to get involved in Erynthul's church, a sort of cold disregard for other people that many people lack, at least in the quantities needed to join the church. The closest thing you're going to find to an accepted Erynthul worship in a neutral community is the Chaotic Neutral raiders who call on Erynthul to let their enemies blood flow like wine, and that's hardly an organized religion...
Of course, this is all opinion, I freely admit, and if any wish to dispute me--please do! I enjoy a good discussion!
Let me give you a quick example, using the PHB gods...
HEXTOR will often have a church in an area. Many of these will be LN churches that attempt to sell him as a sort of uber-disciplined war god, while the others will be vile-tempered LE churches which basically demand that people pay Hextor tribute, or else... Relationships with other, more-hardline churches and priests of Hextor are going to depend on hierarchy and philosophy--for example, the Order of the Iron Fist is a largely LN organisation that sees itself as a monastic tradition training hard warriors to face a grim world. It does not get along with the LE Orthodox Church of Hextor, which is largely backed by the Empire of Asir, a gigantic, partially theocratic dictatorship. The Order sees the Church as giving into worldly politics and losing sight of Hextor's spiritual significance--the Church sees the Order as air-headed fools whose philosophing has obscured Hextor's practical message, which is of course, the Church of Hextor running the show. Still, they can manage an uneasy coexistance, while neither of them can get along with various NE cult leaders who, gathering followers together, proclaim themselves the 'Chosen of Hextor' and proceed to either cut a bloody swath through the land until some hero stops them, or plot in secret to unleash ancient evils/free devils/kick puppies, etc...
NERULL might have a LE church in the area, one that will claim to have given up all the human sacrifice and undead creation parts of the religion, and that is probably lying, though you won't catch them at it. It's quite possible that they have come to some formal relationship with the city government, allowing them to worship their grim god and yet still be functioning members of the community-- serving as executioners for criminals, to give an example. Most of their worship is in the form of 'Please Lord Nerull, don't kill my spouse', 'Oh, mighty Reaper, don't let my children come back as zombies', and the occasional, half-guilty 'Oh Lord of Bones--if Hew the Milner could drop dead--of natural causes, I'd be ever so thankful...' The church is probably willing to shelter less social members of the religion, as long as they don't start any trouble, and move out quickly. It should be pointed out that Nerull's cult has a rival in Wee Jas, and so they aren't always going to have a church.
VECNA will have LE or NE churches that attempt to set themselves up as information brokers, possessers of mystical secrets, and sellers of magical items. They also claim to have given up the human sacrifice and undeath stuff, and some of them might be telling the truth, because these guys are aiming at bigger game. Your local church of Vecna will try to put on a friendly front as they make themselves indispensable to the residents and government--and gather blackmail material. They are very likely to try to come to arrangement with the local criminal element, and meddle frequently in local politics. Naturally, the church is always in danger of being raided by the local authorities, forcibly disbanded or arrested, so they spend a lot of time greasing wheels, and making sure they have allies. They're perfectly willing to channel support to the more extreme members of the religion, but like the Nerullites, don't want them around sullying their home turf. And once again, rivalries and problems with the local authorities mean you're not always going to have a church.
ERYNTHUL usually does not have a local church, since his priesthood are basically serial killers. Usually, his faith is represented by secretive cult cells meeting in basements and sewers, and scheming to kill people. Erynthul is the sort of god that your more civilized sort doesn't like to talk about, or even give money to. I mean, the other evil gods have--some variety. Some ambivelance. Hextor is lord of Force, as well as Tyranny, Nerull is god of Death in general, not just Undead Things That Will Not Rest in the Earth, and Vecna's Secrets don't have to be Vile Secrets That Man Was Not Meant To Know. You can do your business with them and come out unsullied. Erynthul's God of Murder and Slaughter. You maybe toss out a quick prayer to him in fear and anger every once and while, but you don't worship him. It just leaves you feeling--dirty. It takes a special something to get involved in Erynthul's church, a sort of cold disregard for other people that many people lack, at least in the quantities needed to join the church. The closest thing you're going to find to an accepted Erynthul worship in a neutral community is the Chaotic Neutral raiders who call on Erynthul to let their enemies blood flow like wine, and that's hardly an organized religion...
Of course, this is all opinion, I freely admit, and if any wish to dispute me--please do! I enjoy a good discussion!