I would draw parallels with situations where an armed and dangerous criminal is surrounded by innocent people. I believe the police either wait until the situation has changed (while maybe negotiating) or send in people directly who can differentiate between a man holding a gun and a three year old kid. The policemen are taking a far greater risk than they would if they just sprayed the area with bullets from further out but they accept that their job will sometimes involve risking their lives so other people don't die. It's laudable to try and protect your servicemen and women, but if it's at the cost of civilian lives you're doing it wrong.
Legally speaking, for the state apparatus to kill people in a country they are not officially at war with seems very shaky to me, but I'm not a lawyer.
Finally, yes there will always be casualties in war but you can't just shrug and accept it. Only going after dangerous people should be your first priority unless you think increasing enemy recruitment is a good idea. This is a practical point so should be comprehensible even to the sort of amoral bastards high up in the intelligence pecking order and the people who worship them.