They can still be killed though, and that's what the guys at HERO at probably playing at, either join them and become part of the dominant group in the new world or be hunted and die like a dog. Ella's faction doesn't seem to be any better, instead of being forthcoming about their terms and what they expect of the ones that will join they instead lure them with false promises about freedom while in truth they are ensnaring the new recruits with their geass to force them to do their bidding.
The world will probably regress to a more primal state where the strong make the rules and you have to fight to survive from this point on, if you have no powers and no one to protect you, you are pretty much screwed. The governments would sooner strike a deal with HERO or whoever else can provide them with superhumans to fight for them than care about what happens to the average citizens, and I can see a lot more people lining up to receive the monsterfication serum and Ella's pills despite the risks now that it is public knowledge, better than becoming monster food or an easy prey to be toyed with.
Yes. And not only does that make the world an utter hell to begin with, but the consequences of everyone getting powers or dying are disastrous.
First off, it basically wipes humanity as a species, which already is a black mark as far as morality goes. Second, the consequences on social interactions of any kind that stem from everyone being superhuman are basically going to turn the world into an utter inescapable tyranny, or an anarchic hellscape. Third, we were given the info on the survival rates for the process itself, so most people are fucked anyway. Fourth, there is the procreation issue, which even if solved, does not negate the unpredictable but almost certainly devastating impact of everyone now having insane level powers into the future.
Like, I think it's hard to overstate how fucked life will be if things go down this route, given human psychology alone, and that's not taking into account the myriad of risks that come with the whole superhuman deal.
The only possible direction I can think of that leads to a somewhat happy/normal ending for the world, is monsters being removed as a threat, or at least return to their appearances being incredibly rare, destruction of all currently existing methods to force transformations, such as Xanthe's research and Ella's pills, something that permanently downscales max potential of superhuman powers to the equivalent of evolution 2-3, because even all other things aside, having beings that can demolish all laws of nature is going to ruin the world, and of course, annihilation of Ella's entire group and dismantling of H.E.R.O.
Basically, you have to get to a status quo where superhumans aren't going to replace humans, the existing ones have their powers limited, and the monster threat is mitigated, otherwise the world will be so fucked it may not be worth living in.