The British Inquiry (page ~245) concluded that it was likely the hit on Litvinenko was ordered close to the top. Putin was a KGB officer - he now doesn't take an interest anymore?
And if he blew the covers of 100 officers, they would've been under deep cover i.e. not going around assassinating people and going home on the plane.
In the case of Navalny, Putin's main opponent gets hit - if Putin didn't order it, it damages his credibility, I repeat: Whose head is rolling?
I didn't mention it earlier, but Russia no longer has a death penalty officially - this is why Skripal was alive to be swapped. Oleg Gordievsky was sentenced to death in absentia and I believe the order still stands (although hopefully unenforceable)