(1) If Iran really annoys Russia sufficiently they know that the Russians can and will stomp the hell out of them and that no mercy will be shown. None. Mercy is not a weakness that the Russians have. And if they did invade Iran, who would really want to stop them?
(2) An aggressive Iran armed with long range missiles can be used as leverage for Russian objectives.–Ah, those insane Iranians are threatening you? We, the Russians, can reason with them and get them to back down, but in return we want X, Y, and Z for our assistance in restraining them.
(3) A missile defense shield makes the scenario in #2 above less likely or even impossible.

–Get the point?