'Nathan would hit a state where his body just wouldn't be viable to bring back?' So if his body burns out due to his powers, resurrection protocols wouldn't work on him? Why? Does his mind not die or something and just transcend dimensions? If insanity is a foregone conclusion, I get that argument. Then he'd have to resort to suiciding/resetting, and that has some moral reservations.
I think I get what your saying about Cable's new time traveling backstory though. So the recon is that the old Cable we've seen since the character's introduction always grew up on Krakoa with Scott and Jean raising him and hanging out with Apocalypse, then at some undisclosed time left and went back to the future to battle Apocalypse who, despite hanging out with Nathan and having cool character development, still wages war 2000 years in the future raising Stryfe and all that? He just chose not to acknowledge any of that, or his memories degraded due to time traveling too much and forgot he had a pretty good childhood?
So Nathan has to avoid any big changes like getting a cool robot leg to match his arm or getting rid of the virus. Kind of sucks but I got to accept the time travel bullshit that comes with the territory I guess.
The current backstory with Nate Grey/Cable is that every Nate Grey throughout the multiverse will eventually hit a point where his powers grow past the ability of his body to handle it, and the body burns out/dies/self destructs and kills him. This isn't new, that was established a long time ago.
Resurrection protocols are useless in that case because you'd be bringing back a body on the verge of death every time you did it. NO host body would be able to handle his mind/powers once they got to that point. There's no way around that without removing his powers or nerfing them (which is what the virus does).
As for Cable, yes it's confusing. Best way to deal with this is to understand that while past events are currently fixed, future timelines are only "potential" futures and could be changed. As we've seen with HoX/PoX the future Cable was raised in currently doesn't come to pass- earth's mutants are wiped out by AI long before that. So "that" Apocalypse and the one that is/was on Krakoa aren't the same one. They have different histories.
Nate's ultimate mission as a time traveler is to prevent his future from coming to pass (it is a potential future, not a certain future.) if he does, those events don't happen and he ends up with the status of a "refugee" from a future that no longer exists, while his actions in the past of 616 remain canon. Rachel Grey, Bishop, and Spider-Man 2099 are all currently in this category to different degrees.
As for his memories it was established from his inception that his memories had degraded so badly he didn't remember entire decades of his life. The original concept for Cable after all was that he was Cannonball, not Nate Summers- but his memory was so unreliable from his age and time traveling that neither version of himself was aware of it. More on that here
www.cbr.com
Stryfe was a version of himself somewhere on the time line between those two points.