If prone hurts you're not doing it right. If you can't find a comfortable relaxed prone (or any other position) find a coach who will help you.
Try a High Power or CMP Clinic and tell the instructor you're problem. He'll fix you up.
In 1999, my wife came off a colt and broke her back. In early 2003 she was activated for the Gulf War. Like everyone else she had to go to Benning for her pre-deployment work up and like everyone else had to qualify. She couldn't get into a prone position because of her back. I accompanied her to Benning but being an old retired dude, couldn't go to the range with her. I went over to the AMU and explained my (her) problem. I don't know if someone for the AMU did it, or they talked to someone at the range, but they assigned her a coach who got her into a comfortable relaxed position that didn't hurt her back. She said she shot the best score she ever shot in qualifications.
I'm a wimp, if my position hurts or is uncomfortable, I'm going to fix it. Shooting is suppose to be fun, if it hurts its not fun. Not to mention your scores will suffer.
I found that if you get a good position, where you can watch a half hour tv show over your front sight without any discomfort, you're pretty much good to go.