There's a vocal group out there that think social crimes of that sort shouldn't be depicted at all, even for villains.
Sometimes putting racists in your magical elf escapist fantasy is not the way. It's something a lot of folks deal with in real life, and isn't always fun times to put that in your game. Y'know, like how if you lost a parents as a kid it might be kind of not fun to face an enemy called the Orphanmakers. Or if you were intimately affected by a school shooting, you might not have fun with a villain who kills a bunch of children gathered in a place meant to protect them. Just, not really the subject you wanna deal with while hanging out with your buds for a casual Saturday afternoon.
Sometimes, alternately, you really wanna destroy a bunch of racists, and watching them absolutely eat sewer chunks can be kind of a blast.
Depends a bit on the group. The game. The local politics of the time.
Either way, D&D kind of has to deal with the fact that there's some weird stuff in it's DNA, be that racism or sexism or colonialism or whatever. Just like almost any brand that's been around for 50 years. It's some of the work they have to do to revisit old things.
I imagine 5e would keep the Scarlet Brotherhood around, since they are pretty distinctive villains (monks are so rarely folks that you fight!), but they might just not focus whole racial superiority angle. You can make it more of a footnote in their villainy than the whole point of it. They're shadowy assassins who murder people for political gain, they don't have to be actively pursuing a genocide or an ethnostate for them to be the Bad Guys.
Or, they might not even earn a mention. The DMG using Greyhawk as an example setting doesn't mean it has a lot of GH setting elements worked into it. I expect it to talk about how, like, the Free City is a good example of a "home base" for PC's, and here's some wilderness areas nearby as examples of how you'd build out regions with encounters, and here's a dungeon that shows how to do dungeons, and here's Acererak as an example of a villain and how you'd do antagonists in your game...