I don't think Rupp would have much of a problem in qualifying for the marathon and the 10k in Rio. His problem will be in doing well in either if he runs both, unless he just focuses primarily on 1 and does the second as an after-thought.
At an elite level the things one would need to focus on in order to peak in either event, 10k or marathon, are significantly different. Obviously you can be strong in both at the same time, Shorter in 1972 & 1976 or Salazar in 1982, but not be able to fully peak for either which is what is required to medal in the Olympics.
One interesting possibilities emerges though. Rupp could focus on the marathon and simply run the 10k as a fast pace maker for Mo with the outside hope that they could drop enough people that he places well. Mo takes a chance when the Kenyans or Ethiopians can gang up on him and out number him/box him in. Given he and Rupp have two of the fastest PR's, Mo could train for a strength race, figuring the Africans are going to figure out a way to kick with him or box him in at the end, or even if Bekele races the 10k with his strong kick, and then Galen goes out front and hammer it for 6-8k and spreads out the field, then all of the Africans' focus on how to out-kick Mo become mute and team NOP have out thought the competition yet again.