Yeah, officer's to die or not to die issue would have to be addressed. They could die, but there are ways around that for sure...
Skyrim has an Essential NPC system where you knock the NPC out of commission for awhile but they can't die and there's no major reason Alex couldn't go that route. For example when an officer is defeated they are always recovered in escape pods but, if you want to try to explain it, say they've suffered grievous wounds and need 1-3 months to heal. Or, if you suffer total defeat and depending on what type of fleet/faction defeated you, your officers would be captured. All sorts of things could happen at that point: used as hostages and you'll have to pay credits/ships/resources/weapons to get them back, infiltration/offensive with marines to break them out, imprisonment and you simply have to way a long time for their release or hell, if you're lucky they escape in a command shuttle (like the player does) and turn up on some random world/station months later. I'm sure there are plenty of other scenarios you all can think of as well.