So going back to 1975 (when Putin joined the KGB), Wikipedia page "Soviet and Russian assassinations" includes:
Supyan Abdullayev, Vice president of the Chechen Republic of Ichkeria
Vakha Arsanov, Vice president of the Chechen Republic of Ichkeria
Ruslan Gelayev, Deputy Prime Minister of Chechnya
Turpal-Ali Atgeriyev, Deputy Prime Minister and National Security Minister of Chechnya
Abdul-Halim Sadulayev, President of the Chechen Republic of Ichkeria
Aslan Maskhadov, President of the Chechen Republic of Ichkeria
Zelimkhan Yandarbiyev, President of the Chechen Republic of Ichkeria
Dzhokhar Dudayev, President of the Chechen Republic of Ichkeria
Ruslan Alikhadzhiyev, Chairman of the Parliament of the Chechen Republic of Ichkeria
Sultan Ibraimov, Prime Ministers of Kyrgyzstan
Hafizullah Amin, President of Afghanistan
Mohammed Daoud Khan, President of Afghanistan
That of course along with hundreds of military leaders, journalists, and others. I really don't see any evidence that Russia is reluctant to assassinate political leaders when full-scale war is going on. Just because they spared the Georgian president doesn't mean they'll spare everyone.