Not the biggest of deals, but for the record, Raiders of the Lost Ark is a LucasFilm/Paramount property, and Alien is (20th. Century) Fox.
Personally, I would hazard a guess that Disney negotiated the right to use those characters in The Great Movie Ride indefinitely, even if Disney-MGM becomes just The Disney Studios this year. I can't even imagine Disney developing a ride where they wouldn't have the rights to use the character as they wanted until THEY decided they were done with them. But EVEN IF they lose the rights to certain characters/scenes used in the Great Movie Ride, the Raiders & Alien scenes would not be affected in that part of the deal. Now, whether they could lose the rights to those characters in other deals, I don't know, but again, I'd doubt it.