It makes her uneasy that a man she loves can do that sort of thing and she can still love him. When they are away from all that, he is just Draco and he no longer radiates that controlled danger, but when they are in it, he is a weapon, he is heartless and cold and just like a Death Eater, only fighting on their side. It makes her worry about what the war has done to her for that to bother her so little, but despite her ethical worries Hermione is glad she is with Draco. She would rather have Draco, with his disturbing ability for pitilessness by her side, than a bleeding heart who hesitated to hurt or kill the enemy if they had the chance.