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Buddhism does not address ethical questions like this. This question is like asking who to save in the sinking boat. People come up with different reasons based on their biases. Generally Buddhist believe in Dependent origination even though they may act in self-defense. Buddhist also believe in Kamma Vipaka.
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Who cares about kamma in this context? Personally, I wouldn't even care about 'bad karma' if it means to safe millions of lives. If life is threatened I believe loving-kindness is not healthy to experience, but the Buddha is of a different opinion (refer to the Simile of the Saw). There are different rules if one is a monk too, but since monks are also just fallible human beings I would also say that they should by all means stop him (and if necessary) kill him. Not to kill him wouldn't be morally superior imo. If Buddhism is about the reduction of suffering then consequently the source of suffering must be get rid off. This doesn't mean that you kill everyone who is of a different opinion, but it can certainly mean to avoid certain people. The Buddha infact repeatedly said that noble friendship and avoiding immorality and negative people (or people who think and act negatively) are to be avoided, lest one is emulating unwholesome habits