I find it disturbing that Knowledge is only considered evil or neutral.
Knowledge is by its very nature only as good as the people using it.
D&D gives the domain only to two deities: Boccob and Vecna. Makes complete sense why these two get knowledge in their portfolios. But why is Knowledge also not included for a good god? It could and should be associated with a teaching god or an all know god. Odin fills this role in Norse mythology. I see that Pathfinder has used this same method for assigning Knowledge. Prehaps Iomedae, Torag or Shelyn could include Knowledge in thier domains. Iomedae: good governance requires knowledge. Torag: Crafting and Artificing requires knowledge to create. Shelyn: Art is often associated with higher learning. Even if these gods are not a perfect fit, some good god should be. Create a new one. Knowledge is not evil and should not be looked upon as such. Knowledge and Truth go hand in hand.
I don't think the setting should be constrained or modified by this, though. And besides, if anything the Knowledge domain is a neutral domain, not evil; off the top of my head, I can think of seven deities that grant this domain. All of them are at least partially neutral, and only one is evil.