Your plan is just fine - assuming things haven't changed in the last couple of years. We went from St. Petersburg to Moscow followed by the Kiev extension and thought it possibly the best part of the trip. Certainly excellent.
And --- we did not spend the day on the boat waiting for a late afternoon flight to Kiev. We left the boat in the morning, after breakfast and checking out, and were bussed to the Red Square area, where we spent a very pleasant day - leaving sometime after lunch in time to get to the airport. One caveat - some people didn't eat much lunch in the Red Square area and were stuck with few if any rubles to buy anything in the airport, which was a minor problem. Since Kiev doesn't use rubles, they'd spent their supply down and didn't have anything left with which to buy food. For some reason, credit cards weren't usable at the time, etc., but keep this possiblity in mind.