Aside from other responses, I think that you assume that necromancers are raising the dead of souls who worshiped undead worshiping deities in their lifetime.
That's probably not the case - when the necromancer stops by a village graveyard, he's raising the late townsfolk. They tend to worship Pelor/Heironious/whatever goody-two-shoes god that served said townfolk the best in their profession, and not Wee Jas/Vecna/other fond-of-undeath deities.
Now, by raising the townsfolk, you're sapping the goody-two-shoes gods of their worshipers, and draining power from them. You're not touching any of your own worshipers, thereby sapping your own god's power.