A full-size P-90 will not fit into a humbucker hole. You would have to have the cavity routed out (at least in the Y dimension, if not both) to accept a full-size P-90.
If the job is done right, it won't ruin the LOOKS of your guitar. But it *will* ruin whatever vintage value the instrument might have. If that's not a big concern of yours, any competent luthier should be able to make the change for you.
If it's the Phat Cats you're not liking, there are several other winders making pickups that are similar - P-90s in a humbucker size. Gibson's P-94 pickups are my personal favorites, but Harmonic Design Z-90s get a lot of praise around here. Lindy Fralin has recently started offering pickups like these, and there's others as well.
I'm fairly satisfied with the phat cats so far, though I could stand for them to have some lower output. I have a pair of seymour duncan antiquity p-90s in a cheap korean and want to put them in paul since they are my absolute favorite pickups. I'm not concerned about resale value since I don't plan to ever sell the guitar and its already taken the abuse of two years of touring.
I'm about to have a Voodoo (neck) P-90 installed in my Fender Deluxe Tele. Bridge is a Duncan Jerry Donohue. Phil Jacoby (Philtone) will be doing the whole job which will include some routing, but there's already space for a 'bucker, so it should be minimal. I'll post with the results when completed.