Wait wat is someone trying to drug and decapitate a 12 year old girl? I haven't been following properly.
Why not? When Flint was in an emotionally bad state over his failures to save people's lives (people who were emotionally unstable and ended up hurting themselves and their friends), he asked the AM what to do if he had to save someone and if she had any way to stop someone without hurting them or others. And she told him "Just kill them and make sure their head is intact. We can revive them. It's the safest and most efficient way."
And then on Hephaestus someone he considered beaten decided to overload his amp and try to kill everyone, which resulted on lots of people getting hurt because he hesitated killing someone. Said action also proved the danger of amps in a very personal manner, having to outrun a freaking overload inside underground tunnels on foot, starting from ground zero. He rates an unstable child with a weapon of mass destruction who just threatened to kill people for no apparent reason similarly.
And he is slowly coming to terms with the way of thinking that hurting others can be inevitable, necessary or even good, his recent accidental murders and the war against the UWM forcing him to reconsider his values.
And he is generally feeling like crap over various reasons like having killed people, having someone die on previous mission over something he considers his fault, finding out his commander is lying to him and potentially hurting him and others and generally being full of anger and doubt and all sorts of other things that are hidden behind his attempts to stay good, a good person.
So the only logical course of action is to follow the advice given by one he considers a friend and quickly take out the danger as safely as he can for all involved with the only means he knows he has on his disposal (since he doesn't know about Lyra's ability to knock people out, when she said she has venom he imagined she was talking about real venom which could cause brain damage). Once everyone is certain to be safe, he can leave on good conscience and let the people on ship sort it out themselves.
If I just wanted to force drugs on people and then kill them, I would have used my giant robot and +4 Conventional laser.