I don't agree with that characterisation of events. The Mouse Army grew up in extreme conditions, and the Primer tried its hardest to give them the skills and organisation they needed to get out of those conditions, because otherwise they would die. I see no reason to believe that the Primer would not continue to raise them properly now that they're out of that situation, just like the Primer returned to normal for Nell once it had successfully gotten her out of an abusive environment. They're not slaves or broken people.
From my perspective, that characterization has taken on an even more interesting turn now that I have read through a history of Chinese martial arts, and its role throughout the centuries and modernization. Regardless of whether the project succeeded or failed, that subplot was very much in line with the themes and patterns of Chinese history.