You can start the PC's in Keoland and that may be easiest and also most setting-neutral. More people can agree about what is going on there than say in Greyhawk, Furyondy, or Nyrond. Keoland has mostly stayed out of the major wars. If you want to trim back the evil lands, by far the easiest thing to do is take back the conquests of the Scarlet Brotherhood. Many disagree about whether they could have even taken place, because it was all of a sudden. So consider making independent the Hold of the Sea Princes, Onnwal, Idee, and the Lordship of the Isles.
I would keep the villains, though. They are pretty distinguished and fun to build stories around. The thing is, you never know where spies and assassins are. Even something like the Cult of Elemental Evil has spies. For instance, someone rich might move to a land much in need of new taxes and investment, and he gets in good with a local mayor. Then he builds a castle or temple to his chosen god, who is of course the most benign everyone recognizes, and underground he builds dungeons and secretly holds cult services there.
In Greyhawk, much of the adventure is like peeling an onion. There is a layer beneath, then another, and another. You are trying as much to "defeat the evildoers" as learn who they are and what their plans are, and of course, who they're working for, and how their plans connect to others. Well done, Greyhawk is by far the best setting for intrigues like this. The main villains are also terribly powerful, easily on par with the worst of the Forgotten Realms, so taking them down shouldn't be too easy if you know what I mean. (Save that for really high level, if at all.)