Rub rails provide extra protection in the event of scraping and side collisions. It does increase the structural integrity by quite a bit. On the other hand, a school bus is incredibly over engineered. You can remove a TON of the extra structural integrity before being anywhere close to the same safety level as a traditional stick and staple RV.
I personally believe removing the rub rails will be just fine for you. I'm planning to do the same myself.
I'm not an engineer, so take my opinion as worth every penny you paid for it.
hope this helps,