In the manga, there are several corpses in Lavender being used by Team Rocket as ''zombies''.
A bit later, Charmeleon cuts an Arbok in half, though it is shown much later that it regenerated. http://images1.wikia.nocookie.net/__cb20120215011717/pokemonadventuresmanga/images/7/7e/Chap14p12Arbok.jpg
A bit later, Giovanni kills two Magmars with his Cloyster. http://subtlechaos.files.wordpress.com/2011/05/capture10.jpg
I still didnt get to the Yellow Chapter, so i am unsure if there are any more deaths.