ITA re taking a look at the table height.
Also, with doing less at a time.
Two other things .......
* sharpness of the rotary blade -- the duller the blade gets, the more pressure we put on the cutter to do its job. A new blade can make cutting somewhat easier, and less stress on your shoulder/back.
* relax -- sometimes we put more pressure on the cutter than truly is necessary.
And another consideration ... the rotary cutting may falsely being blamed!!!!
Take a look at the ergonomics of all facets of your sewing area (and other things in your life). It could be that these other thing(s) are/have caused the damage and it is showing itself to you when you are doing the rotary cutting; and the rotary cutting not being the root cause.