Regardless of who's idea it was, the killing of Brady and Hindman was a brazen, and perhaps necessary act in the eyes of the Regulators.  If the version holds true that they believed Brady and his men were intending to arrest McSween knowing that the escort by Capt. Smith had not been given as promised, they saw no other option to prevent McSween's arrest and inevitable murder.  I don't believe the ambush was Billy's idea as his position in the Regulators hadn't reach that level yet, but certainly he was a willing participant.  He and the others saw Brady not as a lawman, but a significant thug working for the Murphy/Dolan faction who had the authority of his badge to empower him.