Thor is presumed dead in Civil War, which leads to Tony Stark, Reed Richards, and Hank Pym creating a Thor clone. He shows up during a big battle between the two sides, much to the surprise of pretty much everyone not involved in his creation, and changes the tide of things in Stark's favour. He also killed Goliath, whose death would have an impact on some big events later in the series. Movie Thor, however, is not dead - presumed or otherwise. He'll be heading back to Asgard (where he'll be teaming up with Bruce Banner in what should be a superhero version of a buddy comedy in Thor: Ragnarok), but isn't going to be involved in Civil War. While it's still theoretically possible Stark could create the Thor clone (albeit without the help of Richards and, you'd guess given Scott Lang is on Cap's team, Pym), it's not likely to happen. For a start, Chris Hemsworth hasn't been cast in this movie, and a surprise appearance would be difficult to keep under wraps. Furthermore, a clone of Thor is the sort of the thing you can make work in the comics, but may just be a bit too ridiculous for the movie.