I may take some heat for this, but.........take her to a chiropractor that you know and trust once a month to keep her back aligned. Some people don't like chiropractors, but I believe even the US team uses one. My dd goes to one once a month, and she says she feels better after going.
I wish I knew the answer to this. I worry about this a lot. I go to a chiro myself every once in a while, but haven't taken DD. I do try to keep back work to a minimum by not letting her do it at home or when she is with friends (showing off, LOL). And I encourage her to make sure she stretches well when they are doing back stretches.
There are several things to keep in mind when thinking about protecting backs.
Abdominal/core strength is extremely important.
Also, many gymnasts have an imbalance in their flexibility and strength between the hamstrings and quads. Hamstrings are usually very loose and hipflexors very tight. Strengthening hamstrings and stretching hipflexors and being able to attain and a posterior pelvic tilt is very important.
Hopefully, your dd's coaches are addressing all of these areas.
Correct stretching and conditioning for the abs and back will head off some back problems. Also not trying to push too many big skills too fast---let their bodies grow into the sport
As for chiropractors. NEVER take a child under age 16 to one. The spine of a 6yo is totally different from that of an adult. Chiros are not trained to treat children and a reputable one should tell you this. They also will not prevent any back injuries---just make you feel a little better for a couple of weeks or so.
If your child starts complaining about her back hurting then rest, ice and advil. It may be mild muscle soreness and will go away in a week or so. If it continues and becomes localized, then she should see a doctor.
If you don't see the kids doing much conditioning or stretching then I would ask the coaches about it.