Jlayne… Yes, that is an acceptable solution, but first make absolutely sure your lock is sitting in your mortise correctly. If the bottom part of the lock is not quite seated, it could cause the frizzen to drag the barrel. I would also check to see how much side-to-side slop there is in the frizzen. It is unusual for a Chamber's lock to exhibit any problems of this sort, but it is not impossible. Once you are assured neither of these are the cause of the problem, then yes, it is proper to file or stone off a small amount of the pan cover away.
Matt