I think you're asking for a lot of logic from someone in a pretty stressful situation. At what point do you decide the kids are actually being threatened? When the threat appears, or after overt harm has been done? Carson tried to get Will and JJ to go off with him in his car. How many parents, hearing that, wouldn't flip out? If someone did that to my kid, tried to pick him up and drive him off, and was admittedly in alliance with my sworn enemy, he'd be on borrowed time. I think that Brad realized that the Omega folks (all of them) had just escalated the battle to a whole new level.
I think Brian exposed himself and his true colors when he acknowledged that he was going to keep messing with Brad, Claire, Ace, and their offspring. Do you leave someone like that, who has already created so much carnage, loose?