I recall one of my GBA Castlevania games. It had a save feature that let you save anytime, but just to reboot the GBA. I.e., you could not continue playing after the save, it just saved the current game state and next time you started you could restore that state or load an normal save (from a saveroom). If you chose to load a saved game your instant save was lost. If you loaded the instant save you could continue from that point, but not reload that save again. Iirc. Might have seen that on some rpg, maybe Breath of fire or Golden sun...
This way of saving would solve this dilemma, without ruining the hard work needed to win a mission.