As many times as this particular moral quandry has been brought up in this forum, it still interests me. For instance, why is every comment leaning toward rewrite a renegade response all the way up until you actually make the decision? Nevermind the question about whether you can apply organic thinking to a synthetic issue, the real question might be what makes an action paragon versus renegade?
Most paragon decisions seemed to work on the concept of second chances. Give the Rachni a second chance. Give Shiala a second chance. Even give the Krogan a second chance. In that respect, rewriting the Heretics is about giving them a second chance.
Most renegade decisions are based on not taking chances. Don't waste resources saving the Council, use all of them on Sovereign. Don't waste the opportunity to study the Collector Base, keep it. Don't let Maelon get away with his genophage knowledge, kill him. And don't take the chance that the rewrite can fail in the future, destroy the Heretics.
Majority rules was never going to play a role in Legion's ultimate decision, but the programs working through the Legion platform didn't have time to run through every scenario and come to a consensus. So they made the consensus that Shepard's perspective would speed up the process, I suppose, with Shepard's unique perspective. When Legion tells you there are two more votes for rewrite, we have no idea that was where the wind was blowing for the Geth. For all we know, the majority were in favor of rewrite and that number dwindled as you walked through the station and learned the Heretics were spying on the true Geth. The opposite could have been true as well, with the majority favoring destruction, but the discussion of the loss of the Heretics knowledge and perspective made them think about trying to save them with a rewrite.
Brainwashing isn't a term you can really use for a synthetic mind, not as you would an organic, but it's a close approximation for it. The Geth aren't above using analogies to convey their intent. They will be altering the Heretics' programming. The Heretics had used their own perspective and knowledge to guide their decisions. They will have memory of all such details, but the conclusion will be different. Incongruous. Why did they act in such a manner if they believe as the true Geth do? They will know what they have done, but why they did it will be lost because Legion has forced a conclusion upon them as opposed to their native programming developing it for them.
There is no emotion involved in the decision one way or another. If you rewrite them, there isn't joy in being reunited with their lost programs. If you destroy them, there is no sadness for their demise.
What do you gain by rewriting them? In addition to gaining the programs, the platforms, and their resources, the Geth gain their knowledge. Everything they had done and learned in their separation. They gain a force that had been trained for war, can repurpose this training to fight the Reapers versus Organics.
What do you get by destroying them? The Heretics have likely been tampered with by Sovereign since they joined the Reaper, designed to suit its purposes in a more efficient manner. You reintegrate the Heretics with the Geth, you're reintegrating programs that had direct contact with a Reaper of advanced technological design. That is now in the system. Also, Legion admits there is no guarantee of success with the rewrite. The Heretics might revert to their old conclusion. Worse yet, they may drag more Geth to their cause, now that they share data. Even worse, you don't know when this reversion could happen. At any time.
Giving second chances is also taking risks. You're taking it on the other person's word that they will honor their decision to do better. Such is the gamble with rewrite, but one that pays off if the worst case scenarios do not come to pass.
I wonder, however, how many people would have switched their decisions if the paragon/renegade points had been switched. People want to think of themselves as the ultimate paragon, so they chose rewrite. They justify the paragon nature of the rewrite. Would they justify the decision if a game patch were released that then switched it to a renegade decision?
So yeah, while I'm trying to view this from both sides, you can probably guess that it did lean heavily toward one decision versus the other. I always choose to destroy them. And yes, my Shepard is a Paragon.