I completely disagree with her on that line to be honest. That said, I destroy the base. Not because of some moralistic or ethical statement of principles. I destroy it because I don't believe that the Reaper tech is too concentrated and powerful to be adequately controlled, and I'm disturbed that TIM can't realize it. It's just going to end with someone indoctrinated, and the wrong person indoctrinated could be disastrous. TIM is said person.
Again, remote exploration via mech would have been the ideal approach.
Something else which could be a hindrance, though, is whether the base's automated systems would continue functioning after the purge wiped out the collectors on board. Would the cloning vats simply churn out a new batch of collectors to reassume control of the station before efforts could be made to secure it permanently?
It'd have also been nice to send a probe through first, linked back to base via QEC. Even if the probe only survived a few seconds and succeeded in only the most basic reconnaissance, it would tell the mission planners a great deal about what they were up against.