Nack may not be working for the X-Parasites anymore, but that doesn't mean that he wouldn't be doing them a favor by taking out Samus for them. And besides, it's not like the SA-X really care who does it, so long as she's dead.
Doesn't matter if the SA-X are going to let Nack kill Samus or not. Nack can't take on three SA-Xs at once and survive and even if he could, they'd just infect him after he beats them. To put it simply, he still needs Samus alive to at least finish off the X parasites.
(Though, Ryan may have come up with some other excuse as to why Nack doesn't have to do that).
technically, all he needs is samus blood or body was it was shown that a blood splatter form her could still kill an unshelled parasite.....so uh, he can still kill them using samus corpse
when Samus absorbs X parasites they heal her, so it would fix up her bullet wounds. I'm not sure they could bring her back to life though.
Since Nack is turned away from Samus, do you think that she'd be able to run... well, hide really quickly? Probably not since she's been shot a few times. But maybe Chrono will wake up and carry her off. Or something.
Of course, Nack knows that the moment Samus is killed his own life is up for grabs, yes he could stop the SA-X with Samus's DNA but is he really confident enough in his abilities in just recently gained armor and weapons for which he's had no practice, to take on three copies of Samus, each of which is just as skilled(or perhaps slightly less) than she is?
Nack strikes me more as the kind of bounty hunter who only takes risks when he absolutely has to, in other words when he's lost control of the situation. No doubt he would already have an escape plan for this situation, which would realistically involve, running allowing the SA-X to kill their last remaining predator, and giving Nack enough time to escape, so as far as I can see, at the current moment, it would be best for Nack to NOT kill Samus, at this time that is.
However, how Samus and Chrono are going to get out of there alive, I don't see a way other than a Deus Ex Machina / Plot hole...
Don't you just hate it when someone more dangerous then the person that's about to kill you ALLOWS them to do it? DX