Disney owns Miramax. That didn't stop Miramax from putting out Kill Bill.
I think most consumers won't make the link between Marvel and Disney, just like they don't make the link between Miramax and Disney. The question then becomes: why did Disney purchase Marvel at all? ie: what can be gained? The stock market seems to think not much can be gained (Disney is down 3% so far today).
Marvel owns its own Movie company that has been wildly successful over the past dozen or so years. Also, Warner Brothers owns DC and has been able to turn a tidy profit from the merchandising rights.
Disney's movie company has been wildly successful as well -- so perhaps one benefit to Disney is that they are removing some of the competition.
As for the merchandising rights, you figure that whatever gain Disney gets from this is priced into what they have to pay to acquire Marvel.
Regarding the rides at themeparks, if Disney forces other theme parks to stop the Marvel rides, that means it is going to forego the licensing fees that it would have earned. Sure Disney could build its own Marvel rides, but will it earn more from those rides than it would if it had kept the original licensing deals in place?
I am still not sure what Disney gets out of this deal that makes it worthwhile for them (other than removing some competition).