The question "What would Jesus do?" may be trite, but it's THE question.  Jesus did not teach that we have a duty to accept whatever violence an unjust aggressor wishes to visit upon us.  And you agree we should have an army.  Why, if not to kill?  There's the rub.  It's not having an army that's wrong, or even killing.  It's using the army for wrong purposes, i.e., to engage in an unjust war.  Berrigan failed to distinguish between those issues.

"For the one in authority is God’s servant for your good. But if you do wrong, be afraid, for rulers do not bear the sword for no reason. They are God’s servants, agents of wrath to bring punishment on the wrongdoer."  Romans 13:4.