That's the reason I've never been a big fan of players going both ways. I understand you want your best players on the field, I get it, and it's okay they play the most minutes, but the risk of injury certainly goes up. Sometimes they only miss a game or two like you said, or it's season ending which can really put a team at a disadvantage. How good is that starting player standing on the sidelines? I'd be totally fine with a rule that limits how many minutes a player can play both ways. Not sure how you'd police that other than a hard and fast rule of maybe 2nd string has to play at a given point in a game for x amount of minutes. Maybe 2nd string is for 2nd quarter, then play whoever whenever the 1st, 3rd, and 4th quarter. Gives your starters a break, and gives your backups some reps.