the story is remarkably unclear and tonally all over the place after act 1, and by the time act 3 rolls around, all consistency sort of goes out the window. i don't know if the writers intended this, but the game certainly attempts to frame lucian and dallis as being a certain flavour of 'noble' for what they're intending to do
when really they're just the same old type of "the ends justify the means" genocide advocates who are willing to kill tons and tons of people in order to accomplish what they consider to be the 'greater good' (which the game does not at all make out to be the only solution to whatever problems the universe of this series has), without showing any form of remorse for it. the final scene in particular notes a tonal shift with dallis in particular. she commits some seriously atrocious acts throughout the game that don't accomplish much of anything other than displaying public cruelty. but then at the end she's all like "i respect you and sorry and stuff but anyway, lobotomy time!" i didn't buy it at all. nothing about lucian just showing up sitting in some chair with glowing eyes was compelling either
i don't want to keep disclaiming (retroactively) my criticisms of the game with "i still love the game", but i do think this game is great. it just has a lot of issues writing-wise after act 1. i agree with a number of people in this thread that act 1 did a really good job setting the stage for the game, but then the acts after that failed to follow up in any meaningful way and fall into "you're the chosen one!" tropes real quick
In Fort Joy high judge Orivand transforms a Sourcerer into a Silent Monk instantly just by purging her with a wand. So I don't think it actually requires mind maggots. But since you can craft a mind-control grenade from them, maybe Magisters just use them to turn Silent Monks into Silent Watchers? Most of the monks in Fort Joy are passive while the Watchers are actively fighting for their masters, and maybe mind maggots are needed for that.
i'm pretty sure that encounter makes mention of 'mind maggots', and that they may have already put one in her head, but i'm not 100% on that