It's not the coach's job to consider future effects, it's the general manager's (yours). If you want the coach to play the backup, make sure the backup is going to be better than the starter at some point during the game as the starter wears down. If your starter has high stamina, he needs a relatively better backup behind him, because he won't lose effectiveness as fast.
This makes your team perform better as a whole, and you're not wasting the money you pay your starter, because he's not running around wheezing for air after 30 seconds on the court. It also makes your team better able to sustain injuries, as your team won't have a huge drop in talent because the starter is out for three weeks. The trade-off is, of course, that you have a lower financial operating position, or might even need to retool away from the one mega-salary star and McScrubs model in favor of a more balanced team salary position.
Or, you have the option to only get to start your mega-salary star in one game and play him as a backup in the other game, to keep his minutes under 80.
Basically, the choices are already there, they're already pretty varied, and I don't see that there's anything wrong with the system -- you're just complaining because you don't like the outcomes of the choice you've made. What everyone's trying to tell you then is that you need to investigate the other choices the game makes available to you.
tl;dr version: I'm done with this, good luck to your team.