Well, the thing is... from the mouth of Quirrel:

The pain thing is a bit troublesome, but again, someone like Snape, their greatest abilities can't be unlocked with just pain. As Wedrifid suggests, the pain may unlock some ability... for subtle skilled betrayal and subversion.

And then, of course, he ended up just Abrakadabra'ing her anyway. So the answer actually seems to be that he just didn't care about retaining Snape's loyalty.

That only shows he didn't care about his loyalty that much. To echo Harry's dark side, Snape being disloyal is annoying, but the woman irrationally resisting and sacrificing herself and troubling him was even more annoying.

Also, remember that in MoR, Lily was implied - stated? - to have tried to Avada Kedavra'd Voldemort. All deals are off when one's life is on the line - Lily's life could have bought Dumbledore or the whole Wizarding world! but self-defense still takes priority.