However, I doubt Universal would have purchased any sort of limited license. They probably signed a deal for a one time use for each character they use which a deal like that would hold up no matter who it was sold to. Regardless of who owns Marvel, they have to still hold up previous contracts as part of the acquisition.
That's not how these deals are designed. When a company owns intellectual property valued in the billions (the Spider-Man films alone have made $2.5 billion), you don't sign away a portion of that character's rights in perpetuity.
Some of the relevant details include:
1. What characters are covered under the Universal deal? (I doubt they have a blanket agreement to use everything "Marvel" at their whim.)
2. What is the scope of the license? There is probably some exclusivity clause, but it could be limited to Orlando-area parks, Florida parks, US domestic parks, etc. I doubt that Universal has world-wide exclusive theme park rights to Marvel characters. If Marvel characters have not been licensed in other countries, Disney could be able to immediately put them in DLP, Hong Kong, etc. The lack of any Marvel presence in Universal Hollywood suggests that the agreement may be limited to FL's Islands of Adventure only. Contractually it may be possible to add a Marvel presence to Disneyland at any time.
3. What is the duration of the current contract and what renewal terms are stated? The current deal may simply end with no extension provisions. Or Universal could have the option to extend at a pre-determined price.
Whatever the case, I doubt that Disney would have completed this deal if existing Marvel contracts handcuffed them with terms they were not comfortable assuming. Disney knows that Sony has a contract for the Spider-Man film franchise. They've read the contract and will abide by the terms. And that's true of every licensing partner. But like Iger said, as those deals come up for renewal, Disney will view them from the standpoint of whether they are better bringing the property in-house or renewing the licensing agreement.