I recommend the flash gun.
I was in the same spot as you last year and I went with the gun. My reason was that I wasn't able to get the indoor shots I wanted (even with a F2.8 lens). It was difficult to get great shots especially group portraits. Using F2.8 for low lighting group portrait is tough because the subject's faces are not always in the same depth of field...often I will get a few people tack sharp and the rest will be a bit out of focus. The flash fun pointing to the cieling roughly 1/40-1/120 with F5.6 will do the trick. I can show you some pictures if you want.
He seems to follow my opinion pretty well. I have both of the items your looking at, and IMO, it is what your wanting to do. My 100mm 2.8 macro is my favorite lens, I am disappointed when I'm in a situation that I have to use something else. It focuses excellent and is amazing sharp. However, my flash is becoming more and more valuable to me. I used to try not to use it all the time indoor because it looks so obnoxious, but bouncing off ceiling has become an amazing keeper rate. I'd say before something I'd show or print percentage w/o flash was around %10, now I'd go for 80-90%. Indoor its amazing, I feel like I never want to take it off, it just looks huge for just a few Christmas morning pictures, but it makes a world of difference.
I Love that lens, if your shooting outdoor mainly or interested in bugs, flowers (I found it excellent at the zoo also) out door portraits if you can be far away, then go for lens.
But if you want to force yourself to learn, the flash has a steep learning curve IMO that I have still not figured out much at all. But if you like family pictures, if the wife/girlfriend/family wants more pictures, or if you like to rig up a small studio setup like I've been doing with my wife and newborn, the flash will make a huge difference.
Hope this helped you.