I can't remember whether V ever met Kenny via Eve/Carolyn? But it looks like she was the killer asked by the 12 due to his investigations.
Kenny though knows for sure how Villanelle looks even if they haven't met - he couldn't haev been manipulated into going to the roof with her, would she be strong enough to drag him upstairs (though poss if he was already killed before then)?
But why would 12 want to kill him knowing he's the son of the MI5 boss who were already in the know about them?? They were left alone by MI5, and now Carolyn - and Eve I'm sure - will be onto then like the tom of bricks! Yes Kenny was becoming dangerous but they could have done this further on much more subtly staging it as a road accident he was riding a bike) rather than a blatant nasty murder!
Mind you, they prob know that Carolyn is now under supervision of the creepy new guy and will haev to act secretly again and on her own (with Eve). Still hugely unintelligent not to arrange it as a road accident so nobody could think of revenge/further digging.