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Annie just killed some enemy soldiers who were trying to kill her. It wasn't murder. She had to defend herself. If she hadn't taken care of them there, they would have tried to kill her again later. Whether she crushed them under her foot or made them spin very fast it's not so important. She just used the quickest method every time depending on the situation (and also on a meta level the author had to show some variety).
We can see at various moments during the story that Annie is not a bad person: like during her interaction with Marlo or when she spares Armin's life despite the fact that it could gravely endanger her mission.
The way I see it, both Annie and the Survey Corps are trying to do some good in the world but their objectives clash against each other (apparently at least) and this leads to fighting and some deaths.
It's this contrast between her fighting against the main characters but not being actually evil that makes Annie one of the most interesting characters in the series.
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