He was de facto head of state, was he not? The CIA was answerable to him? (When he wasn't with that woman.)
We've been through this before.
Your irrational beliefs about Clinton weigh heavily on your tapestry of intellectual failure.
The President of the United States is not a king, he and his National Security Council can direct the CIA to conduct covert operations... as long as they are legal. That doesn't mean the CIA won't push the definition as to what is and isn't legal right up to the fine-print - they do, and will continue to do so.
However...
Placing the lives of 800 civilians in danger is not line the CIA will cross, and nowhere in its history has it done so.
And the CIA doesn't tell foreign countries what to do. The CIA makes a case to the NSC, and the NSA runs it by the State Department, and the State Department makes the request. On the flip side, at any point the NSA or the State Department can say no, and the CIA goes back to square-one. This will come as a shock to you, but most European countries don't want the CIA running around doing stuff in their borders. They also don't want the FSB, MI6, Mossad, or any other spy agencies doing stuff either - but it happens. As a result, no country wants to be seen as "CIA Friendly", even our allies.
This has been true since 1947.
The other fact you ignore is that the CIA can tell the President of the United States "No". The CIA and the USSOCOM both told Clinton and his NSA they could not carry out requested actions on multiple occasions. That's on record.
Again, on the night of the Estonia disaster, Yelstin WAS IN WASHINGTON D.C. for a peace summit with Clinton.
Knock off the CIA-Clinton nonsense (they really didn't like him anyway).