I applied for Ukraine this year (Ukraine is the perfect program for me but is also on the non-anticipated travel-warning list like Russia). When I talked to Boren before applying they said that if you apply to one of those countries, your application will be judged normally as if you were allowed to go there. And then if you were selected to receive an award, if they cannot send you to that country they will send you to your alternate.
What program are you wanting to do in Russia? I studied in Moscow last year and its an amazing city. The qualify of life is great and Moscow has, by far, the best public transportation I've ever witnessed. I was taking classes closer to the outskirts of city (MGIMO) and was working nearly full-time in the city centre and still had plenty of time for a social life as well. I hope you get to go to Moscow; you'll absolutely love it.
My alternative to Ukraine was also Kazakhstan. Which program there are you doing?