Litvinenko and Skripal stories make sense. Both were former Russian agents who turned on their old employer. Their assassinations were a message from that employer to the current employees: "this is what happens to traitors, you are never safe even if you retire".
My impression of the Putin's press conference from last week was that he genuinely considers Navalny a traitor. He didn't even bother to deny any allegations about those FSB officers, all he spoke about was how Navalny is connected to the CIA.