Here is how I would have decided to handle the Heretic problem if this was a holodeck-style game of infinite possibilities:
First of all, I’d straighten out the question (in my mind, it might be explained in the game and I missed it) if the Heretics are the result of Hacking on the part of Sovereign, or if they are simply Geth who came to a different conclusion. I think they came to this conclusion on their own, but in my mind this mission is an amalgamation of conflicting spoilers from the comments, my play-through from a year ago, and the snatches of conversation I caught while recording the show.
If the Heretics were hacked by Sovereign in Mass Effect 1, then the virus is more like a patch or an anti-virus program. If so, it’s the way to go to preserve proper functioning of the Geth.
However, if the Heretics are just Geth who have come to different conclusions, then I would strongly advise Legion to get rid of the virus forever. Even warfare is better than the virus.
Humans have the familiar problem that when we disagree, sometimes we conclude that it would be more expedient to wipe out a rival than to persuade them to accept our position. Now, sometimes this is unavoidable. It takes but one side to make a war, but two sides to negotiate. If your foes aren’t interested in listening and won’t accept your difference of opinion, then you have to fight or acquiesce. Unfortunately, this means a lot of our debates have been won with the side who owned the most pointy sticks, not the side with the correct thinking. Any species that grows up in an environment of hostile predators and limited resources is going to have this problem.
So Geth might be facing that ugly truth: They might be looking at war with each other. The standard Geth might conclude, “Look, these Heretics are starting a war with all organics. Now that Sovereign got his ass kicked, we’ve run the numbers, and we think the Heretics will lose. Worse, those organics won’t distinguish between us and the Heretics. They might band together and wipe us out, or at least drag us into a very expensive war. Since the Heretics are the source of the problem, and since they’re weaker than the organics, we should just attack them ourselves.”
You could argue that Legion’s Loyalty mission is exactly that: The first acts of open aggression of Geth against other Geth. A big step for them. The first civil war. The problem began when the Heretics decided to use force against the rest of the galaxy to advance their goals. At that point they became like organics: Creatures struggling to enforce their will in a hostile environment. They left their live-and-let-live policy (remember their first war was self-defense) and entered the fray with the rest of us meatbags.
Really interesting stuff, BioWare. You could do a whole game (or book) on this.
What Legion is talking about is something worse than war. He’s talking about destroying the ability of the Geth to reason for themselves.
War is expensive. Humans sometimes avoid war simply because of how horrible it is, even if they really, really hate the other guys. But flash-drive brainwashing has no such deterrent. There would be no reason to not use it the next time a serious debate arises. “Look, this is too important for debate, just flash ’em and move on.” In a conventional war, sometimes the side with the more correct ideas will win. In flash-drive war, the only ideas that will survive will be those which couldn’t make the cut. As one side loses a debate, their incentive to virus-bomb their opponents will increase. It would encourage the weakest ideas to propagate and the strong ideas to be wiped out. (Or sides would preemptively flash each other, which would be just as bad.) Their debates would be replaced by silent brainwashing. Maybe it would be common, maybe it would be rare, but either way it would lead to stagnation and retardation. The Geth would get dumber every time they used it, by walling off certain conclusions.
This is why it is better to kill the Heretics than to brainwash them. One destroys a few thousand Geth. The other, in the long run, destroys the whole race.
That’s my take on it. Other conclusions are of course possible. You could probably make a very strong case for walking away, or for showing that you COULD have brainwashed them, and THEN walking away. Lots of fun could be had with that idea.