The alternative that I just thought of would be healing any KO'd party members back to 1 HP during the team shuffling. That would probably fix it but might be a little weird.
Even then it'd be risky unless you put some kind of low-health alert in. I kept getting blindsided by Aide showing up to battles at 1hp, I don't have the attention span to remember to heal whoever's rotating in for a boss fight.
Of course, you shouldn't fuss with this sort of thing at this point. The game's been finished for 2 years and it'd take a lot of re-tuning specific encounters if you had to account for players showing up half-dead and resourceless. I only brought it up because it occasionally, and seemingly arbitrarily, undermined the scrambling-to-stay-alive gameplay dynamic that I was otherwise appreciating.