Just to put it into perspective, it was the council races and galaxy that brought the krogan into the conflict. It was the galaxy that determined the rachni were evil, and they still are cautious of the rachni. Ironically enough, the krogan were the only species who actually seemed to respect the rachni because of their strength. Every other species feared them like they feared the geth.
I'd have to do another playthrough. Looking at the Mass Effect wiki, it stated that only one infant in every thousand births would actually survive. That might put things into perspective for you how horrific it was. Don't you remember the krogan females that were committing suicide because they could not bear children? The genophage was not only physically destructive, but mentally and psychologically.
Even if the Krogan respected the Rachni, they were the ones to systematically kill them all and then clap each other on the back and treat that extermination like a feather in their respective caps. I'm not saying that the Rachni were undeserving of that outcome; indeed, an invasion of a highly aggressive species that refused to negotiate could only end badly. I just find it odd how the narrative can have the Krogan cheering each other on for a genocide they committed and have no qualms with it, but when the galactic society implements the Genophage to stop the Rebellions; an option chosen over killing them all just like the Rachni; suddenly its a great evil. The narrative is really indecisive here.
So genocide is bad, but if you happen to look like scary bugs it's okay to wipe you out. But it's completely fine for a highly aggressive species to (arguably) cause more damage to the galaxy than said space bugs in their unprovoked war, but if you implement a method of control and containment on this hyper aggressive species, then suddenly you are the worst being in the universe.
But let's say that BioWare's narrative is right and we should care deeply about the fate of this alien and how unjustly their children are being killed off. If that's true then I want equal priority given to the Rachni children, mentally handicapped children to boot, that Shepard and Co. murder as they go through Peak 15. Heck, our friendly neighborhood Krogan, Wrex is gleefully slaughtering the week old new born without a second thought, plus he argues for melting a defenseless mother with acid. Kinda double standards don't you think?
If I am not mistaken, the chances of survival to adulthood in pre-industrial level was stated to be something like 1 in 1000. I think Mordin says so in ME2. I don't have ME2 on this computer so I can't check, but even if the number is wrong, the point is the vast majority of Krogan children are stillborn or barely gets past the fetus stage, as a direct consequence of the Genophage. There is no possible way I can consider this moral by any means. If anyone attempted to impose this on a human population, I would accuse them of mass murder at best, genocide at worst.
And yes, even if the stated intent of the genophage isn't genocide but "population control", you can't just say (for instance) "we want 99% less Krogan, so we're gonna make 99% of them stillborn, problem solved". There are huge consequences to having a species hit by such a massively dramatic change. ME3 demonstrates this clearly. The Krogans are dying as a race. Slowly, because they live for very long periods and are ungoldly hard to kill, but still. And if the race dos die out, even if thousands of years after the Genophage, it would absolutely have been a genocide far worse than anything humanity has done.
And while, yes, the Krogan did make their bed to a degree, they were still pressed into action against the Rachni by the rest of the galaxy, who did not (apparently) have the foresight to devise containment methods. Because, what with their violent tendencies and explosive breeding, I think the Krogan do need containment. Morally, however, having a strong yet tractable leader that can keep them in check is a much better way than the Genophage.
1 in 1,000 sure looks like a lot, but you have to remember that Krogan females can have 1,000 offspring a year. So one kid a year, that's essentially the same as human women. And therein lies the problem with the Genophage arc, it tries to give human emotional and moral outlooks on a species that is clearly very alien to us.
The Krogan are an R-Selected species, their whole evolution is centered around popping out as many offspring as possible because a very large percentage of those offspring are never going to reach maturity. Really, the Krogan should place no value on an individual until they reach sexual maturity, and can then contribute to the continuation of their species. On top of that, Krogan can remain sexually active their entire adult lives, which as far as we know has no limit. Patriarch, the Krogan aid to Aria in Purgatory was a veteran of the Rachni Wars and he was still remarkably spry despite being well over 2,000 years old. So you have a species that can have up to 1,000 children a year per female, who remain sexually active their entire lives, and could quite possibly be biologically immortal. How is any of this relatable to humanity and our morals?
Even if the Krogan weren't super violent, and didn't cause widespread destruction across the galaxy, something like the Genophage would still be necessary as that kind of exponential population growth is unsustainable. Give unrestricted Krogan breeding a few centuries, and they will overrun the whole of Citadel space with their sheer numbers. You know how in other science fiction settings you have that Horde of Alien Locusts that devour everything in their path, like WH40K's Tyranids? Well in Mass Effect's case that's the Krogan without the Genophage.