Putin does not kill those who make a him troubles. That's not his style. His style is fabrication of criminal cases to send his opponents to jail. E.g.
Mikhail Khodorkovsky,
Vladimir Kvachkov, Oleg Navalny (brother of
Alexei Navalny) etc. He acts in the same way as Erdogan in Turkey.
Also he uses media which he controls to defame whose who he is afraid of. For example, that's how his media shows Navalny (
that man is a worst Putin's nightmare):