Seems that updating the game and starting a whole new playthrough greatly fixed the issue.
In most situations, i managed to talk to Old Bene. No matter if i did the farm quest or not, if i started the children quest or not or if i am wearing the children robe or not.
The only exception was to successfully finish the quest for the children of the Cathedral (distributing the flowers) before asking them about Hanna. It triggers the *error* dialog with Old Bene without unlocking anything with the children.
On the other hand, if i go with Old Bene to fight the children of the Cathedral, everyone else on the map will attack the Old Bene crew, including the actual children (underage characters), and they will defend themselves, increasing my own body count. Even if i didn't kill children, there will be children on my body count (but not the childkiller perk).
When i go back to the main map, the game massively lags. (and sometimes, the folks there attack me)
I managed to save, then quit the game. When restarting the game and loading my savegame, no more lags.
When i go see Old Bene again, the quest reset if i ask for a reward. He send me to investigate at the church where everyone is dead. If i don't ask for reward, he will bring me to the caves.
Anyway, i can now proceed to the caves, and move forward. Still enjoying the plot.
On a side note, i wonder if there was a way to pacifically interact with Stuart Little or if he was alway meant to be hostile.
