I would think your insurance would cover the cost of making it look and function as it did prior to the accident. At the least I would go back to the body shop, point out the problem and have them determine how to repair properly. Maybe they can fix it, or will come to the same conclusion about the need for a muffler. In either case insurance should cover it.

If you are not going through insurance, then it's just a matter of how much of an 'issue' it is with you. The more it bothers you, the more worth the cost to fix.