That would be your problem. Steam automatically backs up your craft files so if you delete them accidentally out of the game nothing is lost. This makes it very hard to delete any crafts already installed. What you should do is to open the game, delete the craft files, and then exit using the main menu. This should keep steam from replacing the crafts. Other than that I would recommend duplicating the ksp folder steam installed and using that to play instead, as that makes steam not interfere, and you can continue to duplicate it to have multiple version to freely mod. Say one ksp folder for Realism overhaul and one for stock.