Not sure if this was pointed in full earlier somewhere but the concept of paragon/renegade is more directed at how you (as Shepherd) acts rather than consequence based. To demonstrate this, there are many instances where you see injustice or evil being commited. The paragon would seek to reason with it, find alternative solutions to violence, save as many people as possible, and only use force as a last resort or if violence was forced upon him/her. The renegade option is to cower down the opposition through force (intimidation or violence) in order to right the initial wrong. To illustrate using a simple example from ME2, Forvan the bartender tried to poison you as he had done to humans before. Obviously that's a crime, even on Omega. The renegade gave him a taste of his own medicine while the paragon exposed him. On another planet, he may have been tried/arrested/executed later but on Omega, the turian shot him. Note that while he died in both, the paragon did not "pull the trigger" him/herself.
Picking Paragon or Renegade options indicates the expression of how you (the PC) wish to solve problems and achieve goals rather than looking at the outcomes from a moral perspective, even though in many choices, morality appeared to be meter by which paragon/renegade is determined. The PC's morality is determined by paragon/renegade, not the overall morality. Both this decision and the collector base decision stem from this logic. As such the decision to "brainwash" or not, the paragon/renegade point distribution has no bearing on what your crew, the Geth, or anyone else in the galaxy thinks. It is an indicative measure of how you (the PC) thinks/behaves and then by extension, this is how you are viewed by the galaxy.
So for my opinions on the matter personally, I took a practical approach. I've played both paragon and renegade games though my renegade games are renegon imports from ME1 so I keep to the same standards. Given such, all my playthroughs have been to "brainwash" rather than destroy, seeing as how more Geth = more ally strength in ME3. I also believe in the notion (already brought up) on Shepherd resolving the Geth-Quarian conflict so he/she gains either one or both as allies.
On all the references made to genocide, threats to humanity, threats to the galaxy, and more, I'd just like to state my opinion that most of them seem to be unrelated and logically unsound to apply to this situation.
Genocide and morning war w/ Quarians? Unrelated issue on this matter. If you are letting that influence you on this decision, then you are obviously biased for the quarians and against the Geth anyways so you are inclined already to destroy them rather than "brainwash/save". If you are biased, then there is no need to discuss whether this is right/wrong, you've already made up your mind on the matter.
A splinter Geth group is a threat to humanity? Really? If Miranda/Cerberus don't think so, then you (the great Sheperd commander) obviously cannot think so either having blasted through them 90% of ME1 and parts of ME2.
Practical logic is the only prevailing one, which states that the reapers are coming.