You're at war. There will always be collateral damage. You'd like to maintain structures and resources, but sometimes all that planning goes out the window when you are fighting. Minimalize civilian casualties (especially, if you are invading to conquer and control). Otherwise, I like the good old saying "never leave man, woman or child alive who can one day hold a sword against you" cuz... fuck'em, they are the enemy.
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Arya is one of my least, if not my actual least favorite characters. I can't wait for her to die (which is confirmed to be coming).