Oh wow, thank you, Thoul.
Like most parts of PSII, I've always wished there was more going on than the little script that was actually in the game. Then again, it leaves the door wide open for one's own imagination! I've had this interaction playing in my head for a long time. I picture Mother Brain has having developed over time a deranged sense of motherly duty to the worlds of Algo, but at the same time, it's not "human" enough to understand what's an acceptable amount of control. Then of course, at some point the Dark Force takes advantage of her system, which sends her further down her warped path.
Game ending spoilers within (can't imagine who doesn't know the ending yet, but just in case...):
I never thought the earthmen were totally evil from the get go, but that as the centuries went by they became apathetic and rather didn't care much anymore what Mother Brain did. Call it "buyer's remorse," I guess, that they thought Algo looked like a great place for them to make a new home, but in reality they were bitter over the loss of their own world and found more jealousy than happiness within Algo. This is how I've always reconciled in my mind how they could just sit back and watch Mother Brain get trashed by the group without intervening at some point.