you can extract non dead bodies (with the balloon thingy), but dead is dead, and ko/zzzz guard can be revived, or it will just get up after some time. Ofcourse discovering a dead body will cause more alarm than sleeping guy too. There is other non gameplay stuff like the scores, different code-names and so on... Non-lethal seems OP at the early stages, but things will balance out later.
You can find new silencer at the field, or call supplydrop with one, or replenish it by returning to the ACC.