Takedowns will not prevent you from receiving the Ghost bonus. I haven't verified it for sure, but being spotted by a turret almost certainly will.
The best way to tell if you're still eligible for Ghost after a close call is to check your mini-map. Any time enemies enter the "Hostile" state, as indicated by the label above the map, you've been spotted and you will not receive the bonus. The "Alarmed" state is when enemies think they've seen or heard something but aren't sure what it is, so causing an enemy to enter that state will not prevent you from getting the bonus.
I'm not sure about Smooth Operator. I've seen conflicting information about it: some people say you get it as long as you don't trigger an actual audible alarm, whereas others say you must not put enemies into the "Alarmed" state.