Isn’t that a staple of the genre? I can’t even count the amount of soldiers I’ve lost to a lethal shot or a Chryssalis friendly hug since I’ve been playing this kind of game.
That is, assuming you have a sufficient headcount to accept losing a soldier.
One of the few games where I’ve actually retired soldiers is Darkest Dungeon. It’s quite simple really, look at the positive and negative quirks, check starter skills, see how much you’d have to pay to remove the more annoying phobias and determine if the positive quirks gained are worth it. But that’s in a game where there’s an endless supply of canon fodder.
I’m not sure how easy it will be to get fresh recruits in PP, so there is that.
And about loss of limbs and disability in general, I can think of games like BloodBowl or Necromunda (GW games) where soldiers/players can acquire lasting wounds, get crippled and you have to deal with it.
You can indeed retire them, you can rethink their role (if your grunt loses and eye and gets an aim penalty, put him on flamer duty, if another gets a crippled leg and can’t move that much, make him a nesting sniper) or you can maybe dedicate resources to acquire prosthetics/bionics or whatever. It also gives soldiers a story.
Even in Crusader Kings, I tend to remember “survivors”, who reign for decades, lost limbs in war, survived plague and “experimental medicine” but lived long enough to dance on their foes’ graves, than good guy billies who had an uneventful reign.
The point is, permanent trauma is a good character builder. It doesn’t have to be overly simulationist and should be enough of a pain in the ass to force you to make choices and rethink your strategy, but not crippling to the point that any injured soldier is a writeoff (although those could happen on occasion to keep you on your toes)