We didn't see the solutions because they're not going to show us everything! It's not Big Brother, it's 20-ish pages comicbooks. You're making up stuff to say that Xavier had malignant intentions for using The Five, that's the headcanon.
We didn't see if they looked for other solutions, and we didn't see that they didn't. It's safe to assume that The Five are the best solution they found.
Why? Exactly because of the reasons you gave. They live in an island full of scientists and reality warpers. It's way more logical to assume that they would have stepped in to propose a solution to M'Day which, until the other day, had literally no easily available solutions, thus the weight of the thing.
Hank McCoy is on that island and he's essentially their head scientist. He studied M'Day and talked to every great mind on the planet including villains years ago. You think he wouldn't have proposed something else if he had ideas on how to restore the X-Gene with their available resources? It's way more logical to assume that he did instead of saying he didn't because we didn't see it on paper.
The Chamber thing, as I've said already, is an extraordinary condition. He was a descendant of Apocalypse and he became Apocalypse-like and it changed his features and we don't know how it affected his powers. We also don't know the further implications of it but I don't think turning everyone into Apocalypse-lite is better than turning them back into mutants without needing to completely change them. That would be pretty invasive. And again, we don't know if it works for everyone.
This is like saying that gay marriages are not allowed because you didn't see someone say they were. If you use this kind of logic you could say anything about Krakoa. And again, seeing the amount of scientists on Krakoa including people who studied M'Day, it would be a better assumption that this is the best they can do. If they had a better and faster solution they'd deploy it since Repowering through Resurrection is bad for the Resurrection pipeline, and they've acknowledged that on paper. At this point you're just making up conspiracy theories.
Oh damn I said I wouldn't fall into the Crucible discussions again