Again, I reject your characterization of Ra's as collateral damage. That's a misapplication of the term, since Ra's does not correspond to a non-combatant. Ra's is in fact steadfastly operating the very thing that it is necessary for Batman to neutralize.
But once the threat posed by the train has been neutralized, how is that still relevant? When Batman makes his decision to let Ra's die, Ra's is merely the former operator of the weapon.
I'm still waiting for you to articulate the exception that applies. Under Batman rules, if you have the opportunity to destroy the weapon and spare the operator, you do. You can't say "I'm blowing up the weapon anyway, so it's okay to kill the operator along with it" if you can spare the operator without jeopardizing the mission.