So, I'm looking at the motivations of our hero to actually go into fleshweaving, despite the fact that it would mean actively harming Aegis, even with how close friends we are, and I can only think of one thing.
They feels they can take a hit for someone else, or that the people need them to be stronger.
Our hero can't stand letting people get hurt, but is otherwise passive and gets strung along for thousands of quests and adventures for it. At the end of the Caitiff saga, we see the hero actively choose to not make a decision, and in hindsight, they almost always do. The only reason they are a hero in the first place is because they can't let people being hurt.
So, Fleshweaver is only accessible if somehow, we feel as if that's what we are doing. So, one idea I was thinking was they don't necessarily consume and kill Aegis, but use their knowledge as a soulweaver to actively fuse Aegis into their body, meaning Aegis would still live somewhat, but the consequences would still be dramatic, as they, along with any other "consumed" spirits would become forceful voices in our mind, and because of our weak will, we could be pulled around in erratic and unhealthy ways. What's worse, this would likely corrupt the spirits we do fuse, meaning that the otherwise friendly Aegis could start to become corrupted, possibly turning from Valor to Justice to Vengeance.
Still a dark turn from us, but it would really drive our major character flaw to home. We get into trouble because we can't say no and to protect others even as it destroys us, and then destroy everything around us, and even making the people we want to protect become monsters.