Most of the time the Dark Lord's followers didn't meet the Resistance members in open combat. The largest of their cells were cleared out in the early days of their government. Hermione had been present at a few of what Antonin referred to as "cleansings'. He never allowed her to go to the really dangerous of them, the ones that her safety couldn't be guaranteed. Even as nothing more than his student and a potential puppet for the Dark Lord, she had been protected. Killing her would've been a boon to the morale of the ragtag group of dissidents who needed to be squashed. He wanted her safe. At the time, she hadn't been aware that his reasonings behind the decision were more personal than professional.