I don't think it will be that big of a deal. Hemsworth was only on screen for a few seconds. His non-Thor-type rolls have demonstrated his limited range. Unless they were going to put him in tights and have him fight lumbering aliens with a hammer, his character would likely have flopped. Chris Pine was ok as Kirk but hardly memorable. After 10 years it's not unreasonable to replace the actor (ala James Bond) or the character.

My guess is they were jockeying for something silly like first billing or highest salary.

The good news is that Abrams isn't directing so this movie has a fighting chance.