When you want to totally exterminate a vector, you need to understand that there will be some “overkill” or collateral damage. The way to minimize that it to convince the “general population” that they need to help you identify those that need to be killed or tried in courts. When those “enemy combatants” do not wear uniforms and intentionally hide among civilians, then you need to be brutal when and where you find them and those civilians who cooperate as shields in hiding them, need to face severe penalties, like imprisonment, or even potential death while performing a military operation against the enemy. War is a messy business of delivering death to an enemy.