mitigate that is to decrease the number of snaps in a game. This has the dual effect of reducing how often you need to rotate players, and also theoretically reducing the risk of injuries as the season goes along.
This isn't something the coaches will ever talk about publicly, for obvious reasons.
I also suspect they don't fully trust JR to run an up-tempo offense. In some situations he's done well with it, but it will tend to put a heavier decision-making burden on him if you do it all the time. Making a lot of quick decisions under pressure is not his strong suit.