Look at it from another point of view - cost and benefit to all sides involved.
Putin
Let us assume that Parshov was indeed a sleeper agent in an anti russian organization (think in terms of a US assasin / agent in AlQuaeda or Al Nusra ranks). Would he be valuable? Immensely! Add to that more hysteria from russophobes, as well as additional leverage in continuing to enforce sanctions against Russia. So the cost is extremely high. What would the benefits be? Killing one of the numerous "witnesses" against an old Ukrainian president that does not control anything anymore gives Russia nothing. Voronenkov was an ex politician and had nothing to do with military, so counter intelligence is also unlikely.
Yanukovich (ex president of the Ukraine):
Cost: Pretty high. As is with Russia, it involves trading a sleeper agent that could be used as a valuable asset to secure position in Russia (due to trading intelligence for favours, money, influence) to eliminate one of the witnesses in a court he can simply ignore. Even if Yanukovich is sentenced to death by the official Ukraine court (although death penalty does not exist there officially, but lets assume that it does), he can simply ignore it and live happily in Russia, and even travel all over the world. Even EU countries do extradition to Ukraine only on the basis of goodwill and unofficially. So he is probaply safe unless he drives into actual ukrainian territory. So gains for Yanukovich are also marginal at best, while costs are probably the highest of all parties potentially involved. We can assume that Russia might have sleeper agents in hostile organizations. But for a person out of power and in exile, they would be much more valuable, no?
Ukraine / Poroshenko (current president):
Costs are minimal. National Guard is one of his pet projects and has an abundance of fanatics. More so, these are mostly anti Russian, so persuasion of killing an ex russian politician would not be a problem. Especially considering that the actual killer (Parshov) was in the war zone, combating pro russian forces and was wounded in battle. Was Voronenko (victim) valuable as a witness? I seriously doubt that. This court is a farce and has no actual power in terms of inforcing it's decision. More so, the so called witnesses are numerous, including members of Yanukovich's government when he was in power.
Benefits include another spike in anti russan publicity, another trump (no pun intended) card in favour of anti russian coalition and sanctions. If by this murder removal of sanctions is postponed even by another month or a week, this means huge amounts of money for all parties involved. This is valuable! Valuable for Ukraine in terms of improving its own economic situation (even by a little) as a whole, or several businesses that gain benefits from sanctions on Russia in particular. More so, this could be a favour for some third party that needs to keep anti russian movement rolling in Europe or the US. And again, this is valuable, it can be traded.
I am not saying that I am 100% correct. But most of these things can be traced to their original source by following a cost-benefit reasoning, just like in any criminal investigation. And to me it looks like Ukraine has more to gain from this assasination than Russia, Putin or Yanukovich.