But the Russians have no motive to go around killing Iranian rocket scientists, unless they want to blame it on Israel, in which case they would have used the usual Israeli MO, as you said. Perhaps Israel wanted him dead for obvious reasons, but used a Russian MO just to muddy the waters. But they’ll probably blame Israel anyway, because that’s how Iran rolls. So the waters remain un-muddied.
Countries spy on each other. Even allies spy on each other. That’s because, as Churchill pointed out, nations don’t have friends. Nations have common interests. Quite frequently nation’s interests’ clash. If the dead guy was selling information to the Russians, then he might have tried to hold something over his “control.” You give me more money, or I do X, sort of thing. Granted, that’s a low probability. Also, don’t discount a jilted love, a homosexual affair or any number of domestic things that can also lead to death.
One way of cleaning up loose ends, think the Clintons, is to do away with the people who have the information that may be damaging. In the case of the Clintons, probably they’d all be alive if they hadn’t tried to turn their knowledge into profit instead of just spilling the beans. That’s the problem with people who get involved in questionable transactions/interactions in the first place, they do it for profit. In the end, it would have been better to take a loss and be alive than to have some knowledge that would be inconvenient to the Clintons. (Or any similar criminal enterprise.)