Philosophy and mathematics aren't even on the same field. The stargazer asserts that, in its observation of the universe, organics have always created synthetics to be slaves, and when the synthetics became self-aware they rebelled against being treated like farming equipment. Noting this pattern (and by conjecture having participated in the pattern in its own original galactic cycle) it sought to end abuse of synthetics by not allowing a race of organics to cause another cycle of genuine near-extinction of not just space-faring sentience but life itself. Simply put, this argument can be narrowed to good ol' D&D alignmments. A Lawful Good god will presumably be more than willing to sacrifice some life if it means preventing utter extinction; doing the most good in the most orderly and calculating manner. Basically, if unleashing the Borg would allow the god to prevent a Skynet incident on a galactic scale, it's a tally of which outcome would be the least unfavorable and to enact it. Remember this, and you may not have found this in ME1 unless you did a lot of exploring: the Prothean datasphere you can find shows you that humanity was in the stone age when the Protheans still existed. Therefore humans weren't a threat. Assuming what the stargazer says, that would mean humanity would never be a candidate for destruction as long as they weren't a space-faring civilization capable of producing sentient AI. It is using the mass relays which dooms a culture, not being sentient. While the stargazer is biased by being an AI and sympathizing with oppressed synthetics, it is understandable that it reached the conclusion it did. The Reapers and stargazer are what the Geth could become, I thought the parallel was clear.