I don't agreed with the exact plot if the OP, but I do like the concept of an assault and extraction type operation. Rescuing a captured group of troopers and then having them assist you in the escape. Having one of the rescued troopers die would be a wipe.
Those missions are the worst in all other games, why would it be any better here?
Most players hate the protection missions where you lose if the NPC you're protecting dies. Probably because that NPC tends to run directly into the line of fire and has no sense of survival (think Natalia from GoldenEye).
A rescued trooper squad that helps you in combat, where only one of them dying causes a wipe, would make that worse.
Instead, have a bonus associated with the number of them surviving. Biggest bonus for all surviving, no bonus for none surviving (or for less than half surviving).