I don't think the Kremlin believed they had a realistic shot at Trump becoming president, I think their plan was merely to sew division and doubt amongst the electorate, to smear Clinton and encourage hyperpartisanship. Discrediting the American political system by Trump contesting a failed election, by painting a picture of rigged democratic primaries, rigged media, and all that shit was "the plan".
Him actually winning was just a success beyond measure, and now as you say there is no good outcome. If he stays on, major damage done. If he steps down amid conspiracies of dirt, damage done. If it all goes public and he is thrown in goal, major damage done.