I am not a lawyer, but there's a chance things have changed.
Based on my reading of the contract between Universal and Marvel, if a third party comes to IoA (read: Warner Bros. with Harry Potter) and gets compensated based on park attendance/revenue/etc. (do they?), then Marvel must be offered the same deal. Granted, I am a bad reader, and this depends entirely on how the HP deal is structured, but I'd bet that WB was favored heavily in that particular contract.
Also, I'm not sure if I misread the exclusivity section as well, but Disney might be limited to using Marvel only in California and Paris. Japan, Hong Kong, and mainland China are all part of one region in the exclusivity shrinkage of the Marvel contract, assuming that The Amazing Spiderman constitutes something of comparable scope to Marvel Superhero Island (I argue that it does, and the fact that the ride in Tokyo opened nearly 5 years after Marvel Superhero Island suggests that Universal would argue the same). Disney's bailing out potentially 4 resorts by buying this contract out.
EDIT: Skimmed the Harry Potter contract. They get a flat fee annually and a cut of merchandise. I don't know what that means for Marvel/Disney.