Drilling and tapping is probably your best, if not only option to repair this. However, this doesn't address the underlying issue that caused this in the first place, so you would only be doomed to failure again. I think what you need to do is brace the muffler properly. I'm guessing you probably didn't do it in the first place, and if you did, you didn't do it well enough. You need a bracket that supports the muffler itself, and ties it to the frame, so that it's entire weight isn't hanging by only those two bolts that hold the pipe to the head. Mine came with straps for that, if you don't have those, plumbers strap would be my go to, it's cheap and versatile, I always have a roll of that stuff around, since it comes in very handy sometimes. You just need to support the weight of the muffler from the muffler end.
Just imagine yourself grabbing the end of the muffler, and shaking it as hard as you can, if that seems like it would break it off the head, that's because it probably would. But if you secure the other end of it, then that is an entirely different matter. Without support, the thing is acting like a big lever, applying a bunch of leverage to pulling those bolts out.