Ordinarily, if you want your character to be able to scale, it's good form to prepare for that in advance... but it should be possible to fix it up.
Unfortunately it's very difficult to generalize the solution. There are as many potential solutions as there are ways to create the problem in the first place; which is to say, possibly an infinite variety. And we can't guide you towards the right solution(s) without a more specific understanding of your current situation. Try to give us specific details on how your character is rigged.
Is it smooth or rigid? If rigid, are there flexors? How about lattices? Blends? IK solvers? Are you animating on control objects, or raw joints? Or both?
If we can identify the situation specifically, then it will be a lot easier to approach the solution.
Also, don't forget that if it's a simple scene, you could just scale the scene =)