I just went in guns blazing and wiped him out entirely. I didn't really see any other way, because my companion refused to go with me peacefully and I didn't want to leave him behind. I only got one quest failure (I think it said "Et Tumor, Brute?") so does this mean there aren't too many consequences to resolving his fate the violent way? It reminded me a lot of taking down Metzger. Pretty cool.