It's all about balance. If everyone's life must be good, what even is good enough for the best of them? And who's soul shall be put in the least desirable lives?
MC is disrupting the natural balance, and I could see why there would be an effort to take him out of the equation (if the writing on this series were better, their means and motives would be better explored though), but actively intervining in the lives of the others as well is a different matter. Those are very problematic actions for deities, for sure.
Well, that would make sense... if the MC would be active in EVERY world but he isn't.
The MC only lives in one world and even there he only affects the lives of the people within a certain area around him.
So with there being multiple worlds and therefore billions, trillions or even more lives to be reincarnated into there should be enough possible choices for those souls to be reincarnated into.
Therefore rather than disturbing the balance I think it is more likely that the author cannot can think of any other "mastermind" / cause for those large scale issues other than the "gods".
After all, whatever the reason would be supposed to be, it would have to be so powerful that only the MC with his abilities can take care of it.
Otherwise the issues would be solved without the MC and hence not appear in the story.
But the MC has powers by now rivaling or eclipsing some "gods" already.
As such the author cannot just name some monster or natural disaster as the reason because there would either be no need for the MC's powers then or the MC would simply solve the issue with a clap of his hands.