Legion staffer here. I can't say whether Legionnaires got infected (not because it's classified or anything, I was just too busy not dying myself to notice one way or another) but without TK or force fields or something, the only way to stop them was headshots. So yeah, there's a decent chance any given Legionnaire had to kill a friend, and we didn't know at the time that we'd be able to bring anyone back afterwards.

I haven't slept without tranquilizers since, and I didn't even see any fighting.