That sucks. I had a bug similar to that happen to me a while ago when I was landed on Ike, but the kerbals somehow were changed to debris instead of eva. There might be a way to regain control of them, but it would probably require some messing around. For my problem, I just terminated the ship and the kerbals and revived the kerbals through the game files, although there probably is a better way. Also, are you using any mods? I think my problem was with a glitch in the kas mod. Anyway, if you don't care about saving the ship, use the method I used. Otherwise, I'd just try some different things and see what results.