What happened here was:
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Chompy wrote a very believable reaction by the governments of the world - survey these people and so on. That's perfectly coherent and realistic. That the morality of said methods is questionable is also perfectly coherent and realistic. Basically, Chompy, as always, wrote perfectly well.
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Lucas, a person with a distrust towards militaries, found out. From her perspective, they repaid her saving the world by spying on her and did the same to Lilly and even to Jon/Jen. Moreover, they stole technology from Lilly that Lilly had created and that was not supposed to be used for military uses. This pressed all sorts of buttons on Lucas, who, in these matters, has no shortage of them.
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Lucas proceeded to go ballistic because she sees overreach by military types as a threat to her very way of life due to Brazil's history. Right or wrong, her reasoning goes: "If they are willing to intrude upon my personal rights, what's to say they won't be willing to coup out a government they dislike?". She proceeds to act on this reasoning via a HUGE show of force. Likely counterproductive, yes, but, and I cannot stress this enough, seemingly validating the prejudices of someone that has a lot of power and fears the kind of thing your group has a history of doing in her country is a bad idea.
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This is basically what Makepeace did. And it's okay storywise for him to do it. It very much is the kind of thing people in his position, even the nice ones, would do. However, this doesn't really matter for Lucas. Right now she cannot really see him as the guy who (and I myself wrote that) saved changed people from prejudice and so on. Right now, she sees him and his platoon as... Well... Less than vermin.
Chompy wrote a situation that is perfectly coherent. True. Lucas's reaction is that of someone that hugely distrusts military types and found out she had her privacy invaded by them not an hour ago in-story. By her standards, she's showing restraint.
Even assuming the actions by Makepeace are morally a-okay (it is arguable, though I for one say it at most is a very gray area), it turns out that the person who fears overreach by militaries more than anything won't really see it this way.
Again: it is to be expected for large countries to do this kind of thing. On that matter, Chompy was brilliant, as usual. Lucas's reaction in-story is to be expected as well. Because, well... They tap-danced on her berserk buttons. :p
