It's not that uncommon - what you're going through. I would pull the section on the other side a bit off the forms to establish a bit of symetry (if you can with no hassel). It's probably above the waterline. Your boat is not going to paddle bad, Matter of fact you may have improved it. Trying to force it back could just cause you a lot of headaches and if you crack it or try to cut in you just create a monster project over nothing.

There's loads of tolerence on the engineering of a kayak. It's more art than science. The kayak will paddle perfectly.