Still learning to navigate the Fed rulebook but I only see a carve-out to return runners to TOP for an uncought foul ball (8-2-9). Otherwise the closest I can get is 8.4.2 Situation R:
With R3 on third base, R1 on first and two outs, B5 hits a fair slow roller toward first base. B5 interferes with F3, who is trying to field the ball. However, R3 scores before the interference. Does the run score since R3 touched home plate before the interference? RULING: The run does not score if the runner advances during action in which the third out is made by the batter-runner before touching first base.
I agree completely with @johnnyg08 that the logical ruling would be to not count the run. With that said, with less than two outs I like @jimurrayalterego's solution, but with two outs and no possibility of a double play I can't find a way to either get R3 or BR, and I don't see a way to avoid (unhappily) scoring the run.