Ya know, I feel like the renegade and paragon options on this mission are a little screwy. Personally, I find it infinitely more morally questionable to reprogram the Geth's free will than to blow them up. The ONLY reason I went with the reprogram option was because I needed the paragon points to settle the dispute between Tali and Legion peacefully.
So it's Renegade to blow someone up while Paragon to rewrite their minds to make them think the way you want them to think. Okay, were the writers even trying to have a consistent morality in these games?