In ME1, Wrex sees his people as a lost cause. He doesn't think that the genocide is actually fatal to them; he's of the view that it's their nature that brought them down, and nothing can change that because he tried and failed.
In ME2, Wrex is suddenly a leader again, and embraces his vision for a new future for the krogan - one where they overcome the genophage by doing what they should have done in the first place: build a society, as best as possible, and work to overcome their bloodlust. He's not perfect, and not a moral paragon, but he seems to accept the genophage and believe he can build a new future for his people.
In ME3, he's obsessed with curing it, and basically turning the krogans back into what they were. But his whole point before was that the krogans - albeit victims - were leading themselves to extinction because of who they were, and that to save themselves they needed to change. This just screws with the whole moral arc.
This is what is fascinating. The Krogan are portrayed as victims of the genophage which they brought upon themselves by attacking the galactic community. You were brought face to face with it during Mordin's loyalty mission on Tuchanka. You met the Krogan. They would burn their entire world down again - the Shaman said proudly, because the harshness of the environment on Tuchanka is what now keeps the Krogan strong. Then in ME3 Wrex wants the cure for the genophage if the Krogan are going to enter the fight against the reapers, even though he knows that all is lost anyway if he doesn't. 67% of people cure the genophage even though the end result is over 16 trillion in 300 years.
Now, we turn to the Quarians who created a race of synthetics that nearly wiped them out and took over every world they inhabited, and forced them to live in a deteriorating fleet of ships. The quarians are forbidden by treaty with the Council from taking any action in the Perseus Veil for fear of antagonizing the Geth. But when they finally have the means to take back their home world, they do so. The reapers have also invaded at the same time, which means that the Council won't bother them. They have not attacked any council world. But they're being seen as stupid pains in the ass.
You know the Krogan would need to expand, right? But there are only so many garden worlds. And they are occupied by other races. Eventually that means wars.
So the blackmailing of the galaxy by Wrex with a solution that will overpopulate all of the garden worlds with Krogan is fine. The Quarians trying to take back their home world so they could drop off their civilian population, and join the fight against the reapers was looked at as bad. My guess is that the latter involved a synthetic race that they created. But it was still home to the Quarians.
Now there is another way of looking at the Quarians' action that was never considered. They did the galaxy a favor. Do you really think that the Reapers would have allowed the Geth free will? Do you really think that the Reapers wouldn't have hacked the Geth servers and gained a huge synthetic army for themselves? Maybe by the time the Quarians got into the Tikkun System they finally did? Sure, Legion tells us the single reaper ship made the offer and that the Geth refused it until "the Creators attacked." But this is where there's a huge plot hole - I'm looking at you Patrick Weekes. The reapers never make an offer you can refuse. That was done strictly to manipulate the player into this artificial moral dilemma. And the player chooses to accept that Legion is telling the truth that only after the Quarians attacked that the Geth accepted the offer of the "Old Machines". Legion later, if the player chooses the renegade dialogue, admits to lying over and over again. But most players mindlessly hit upper right dialogue all the time because Bioware games reward upper right choices.
Perhaps what you're doing is shutting down the reaper controlled geth so that you can finally get to the reaper, kill it, so that Legion can finally do what it wanted to do the entire time: create its own race of true AI synthetics that were not Geth at all - they only looked like Geth. You allowed Legion to completely reprogram them. You have to remember that the Geth are software. Legion completely overwrote their programming - no more runtimes. Now a completely new AI program in each Geth platform. The Pinocchio Program. These are no longer Geth.
This is worse than rewriting the Heretics and changing their opinions on the reapers. This is fundamentally changing what the Geth are. The Geth were a networked intelligence. Legion is killing that. By allowing Legion to upload the code you also destroyed what the Geth were. So is letting the Quarians finish off the Geth any different? No.