I have this ending in mind but it's for oc

Ordinary mortal facing against 2 son of god reincarnate where he wishes to shape the world he wants to live in that's the polar opposite of the world 2 son of god envisioned.

The removal of chakra is but a band-aid at best, as the knowledge of chakra are still being monopolized hugely by the clans and their respective hidden village so the impact is focused only on their own group, the one that's worked together to fight against a self-proclaimed god only to find 2 of their central figure are playing god against them right at the end and end up hurting their life the most, kinda dick isn't it?

cult is a no-no, you're essentially forming a group of 'chosen people with power' with the sole purposes of further brainwash & suppress other people to follow their ideals, what's the difference?

and some plot point you mentioned won't happen simply because Ninja even if they're the cornerstone of the story they aren't the foundation the world runs on. so no the economy still running, daimyo still strong because yeah losing huge amount of elite ninja might hurt but they still has personal army more than ten times the amount and the peasant conscript that has even bigger number.

intention might be good but the execution kinda iffy. But just remember that even if taking guns away from people won't prevent someone kill another person in spite at least it lessens the damage it may cause.

there's more step one must do to prevent the loss of life, but taking away the weapon that can cause many of such loss might be the important first step.