I don't think I ever heard that a deal had been reached with the owners of the original theatre, to allow Disney to use the theatre's likeness as a weenie.
My memory isn't always the greatest nor is my knowledge of all things theme park encyclopedic ... it could be that either the story about the weenie-licensing conflict has been exposed as a hoax, or perhaps a deal actually has been reached. But if the story still stands and a deal hasn't been reached, then the stage will pretty much HAVE TO hide the theatre.
I do know that in the field of photography, there is a growing legal chill against ever using ANYBODY'S identifiable building, structure, or any of their property as the main subject of any commercial photo without the written permission of the building/structure/property owner. Photo agencies therefore state that they will reject artists' submissions of commercial stock photos if there appears to be anyone's identifiable property in the photo.
The idea that the hat was built to block the view for legal reasons is very likely an urban legend. You can read a good article about it here:
http://www.yesterland.com/removehat.html