Finished the game yesterday and I don't think this will brick everything, although some specific stuff could be easier / bricked / kinda funny. I just hope you got the loot off of them.
Please let us now, how this plays out.
spoiler main story
He's not a central character to the story, but he has an item that can be change the main story significantly. Afaik there are two ways to get it, the one where you fuck him over should still be possible.
the character's death according to DnD lore
Raphael is a devil, so he is not from the material plane, but from the nine hells. In DnD, if you kill a devil in any plane other than the nine hells, they just kinda reappear in their home plane. This mechanic is actually being leveraged by larian for another quest in act 2.
So if he reappears, technicially it wouldn't be wrong. However I'm really curious if he's gonna acknowledge this. The next time I saw him after Wyrms Crossing, he kinda wanted to kill me anyways...