I think the cannibals just take over, they don't play in wiping them out.

It's like how Catun gets taken over by fishmen if you wipe the UC.

I think the biggest issue to the HN with the Flotsam, is that it's not just a 'faction', it's a movement.

As in, it's not gunna stop if they wipe out the Flotsam, it's their treatment of their own women that made the Flotsam, and that will continue until they stop their shit basically lol, just like real life.

There are notes in other HN cities etc. not connected with Flotsam at all, about other women in their cities forming rebellions and similar. Taking Flotsam down would stop it somewhat for the immediate future, but not long.

As for the discrimination, religions change overtime and changes will happen to Okranism if necessary.

Right exactly, and it takes stuff like Flotsam and so on to do it. In real life its not so much about combat and fighting and killing (thought often still is, look at what's going on right now in Europe), but oppression and so on always breeds counters to it.

People want to be free and all that.

A lot of the notes even say as much;

All I ever wanted was a chance to choose my life and be considered a person, not like an animal without reason.

https://kenshi.fandom.com/wiki/Letter_To_Moll

You can't beat ideals like that into submission. They'll never cease.