No, Annie headed for the open battlefield because it would prevent the human soldiers from attacking her (no high places for 3D maneuvers) and because she needs a bit of room for her trained and sophisticated martial arts moves. If she had any thoughts about avoiding extra kills, it was of secondary importance. She has been killing ordinary grunts so gleefully she doesn't really consider each and every human life sacred. Only her "friends" mattered.
I find it hard to believe Eren wouldn't realise, at least before and after. Hard to say when he's in a berserk mode, but probably not - since he's in a berserk mode and berserks aren't known for thinking too much when fighting. It's enough if he knows afterwards because he will always be in a position to decide whether to keep fighting in the future or not.