Clearly, Andromeda served her purpose. There was no reason to allow her to continue living. Hermione no longer doubted that Antonin's accusation was correct. She had ample reason and opportunity to kill his mistress. Just because she didn't remember the event didn't mean it didn't happen. She would have to retrieve her memories from that day. Why did she kill Andromeda beyond the simple fact that she loathed the ground she walked upon? There had to be some clue she was missing. Even in her line of work she didn't kill someone just for the hell of it. There was always a reason.