The best chance Universal has of arguing they're control of characters in GoTG universe is The Collector, Drax and Groot. Drax was a major player in the Silver Surfer comic in the early 1990's, Groot was a villain for Hulk, and The Collector's entire history is based in the Avengers which in my mind leaves little doubt that Universal would win that one. Current rumor holds that the attraction would be based on The Collector's base, and if that holds true, that would be Universal's best argument for stopping the retheme.
It'll be interesting, that's for sure!