I just don't think that the bane ability should stack with Greater Magic Weapon. Of course, I'm not saying I'm right, and I can certainly see the logic reasoning why it should:
GMW (via Magic Weapon):
"Gives a +1 / four caster levels enhancement bonus on attack and damage rolls." Note: technically, this does not say it grants the enhancement bonus to the weapon, but it's not too much of a jump to assume it does.
Bane:
"... its effective enhancement bonus is +2 better than its normal enhancement bonus (so a +1 longsword is a +3 longsword against its foe)." Note: "its" in this sentence does specifically refer to the weapon (but the technicalities are not my argument).
In my opinion in this situation, the longsword has a +3 enhancement versus giants. Since the GMW spell grants a +4 bonus, it supercedes the bane bonus.
In conjunction with the secondary question concerning epic damage reduction, I think it's a bit cheap to bypass epic DR with an ordinary magic weapon plus an ordinary (high caster level but non-epic) 3rd/4th level spell.
Just my opinion, please don't bite me too hard (although I'm willing to take a few hits seeing as I'm the only person thus far to see it this way

)