There are two main problems with gel--
1. They don't breath, so in the summer, your horse will be DYING from the heat.
2. They're usually heavier then many other pads!
With that being said, back soreness is a huge issue, and I would get a chiropractor or a massage therapist out to check on him. If it's not fair to make a person run when their leg hurts, then it shouldn't be fair to ride a horse when his back hurts.