The only thing about finding a 90 lb trainer is that its very hard to do. We sent our 12hh caspian mare to a trainer who was 100 lbs and she was the smallest in the area for about 150 miles.
I do agree that she might not hold up if she has weak conformation, and its always the risk you're going to run just like with poorly conformed full sized horses- which is why I suggested that OP give us a picture of her pony before I actually tell her to go for it. A weak backed, weak coupled, twisty legged pony probably isnt very sound for ANYONE to ride, but a short backed, strong coupled pony with at least decent legs should be just fine with precautions, sensativity, and moderation :)
Here is a picture of our mare that is about the size of yours OP. She is 15 and has been ridden since she was 3 1/2 4-5 hours a week in lessons for kids, and occasionally (about twice a month for tune up) by me. So far she shows no signs of swayback, artheritis, or weak ligaments. I've never seen her go lame except for once last year when we realized that she has a muscular problem that causes her to become very tense if not let down slowly from a ride and being warmed up well. As long as you give her time to warm up, she's never had another problem. A lot like a runner or a swimmer who doesn't stretch before racing. Her conformation leaves a lot to be desired, but properly muscled she seems to be just fine.
At a rodeo parade last year- pictured with a 5 year old boy on her, next to a 35" miniature horse.
4'8 little girl on her, about the biggest we allow for lessons.
The hill work you're doing with her is perfect and will really help her. Start trotting her in hand up the hills as well once she can do a walk easily. Flexation exercises will also help her tremendously, I think.
Even if she can only be a cart horse, don't let that deter you! My mare is only 34" tall and I LOVE to drive her. My favorite thing to do is take her out on the wide trails in our area to drive, having her do obstace courses (wide set poles, bridges, tarps, etc in the cart) and just going on pleasure drives. You can do quite a lot with a well trained cart horse, suprisingly!