I know that Tomorrowland is a far cry from what it was in the early to mid 90s, but is it just me, or is Guardians a better fit here? Guardians takes place on several different alien planets (like the planet that Tomorrowland was supposed to adhere to), and it makes more sense for it to be there than MILF.
If Disney is so set on keeping the Collector, just turn it into one of his galleries. You can keep Skippy that way (and maybe even bring in Howard the Duck or Cosmo the Space Dog). I'm not sure what the exact plot of the attraction would be, but it could be something like "The Collector invites you to visit his collection of alien beings" or something, and different aliens could pop up where Stitch is now. It could be terror-and-seatbelt-free. Nothing even has to go wrong until the end of the attraction. The last alien that the Collector brings out could be Rocket or Groot (...or Rocket and Baby Groot). Warning alerts sound, seats rumble, The Collector says something about intruders, lights go out, you hear glass shatter, Star-Lord/Drax/Gamora's voices are heard, and when the lights come back- Rocket & Groot are gone. The Collector apologizes for the trouble, and you're ushered out the door into the gift shop, where you are surrounded by Baby Groot merch.
Other than having to make a few new AAs, hiring the GOTG cast, and getting rid of all of the seat restraints, this sounds like a win/win for the parks. We don't have to worry about it being in a location that it shouldn't be (the discussion about IP in Tomorrowland has passed), and Disney makes money selling Baby Groots.