I would make my decision based on what our teams tendency is hitting with RISP. if we are hitting with RISP as we are in may i'll take the 2 doubles but if it was April I would take the HR since it is a minimum of 1 and the doubles would have to score with a hit with RISP to net at least 1.
Jacko also brings up a great point that it would have to be 1-2 with a HR or 2-2 with 2 doubles. Take game one of the doubleheader vs. the Tigers, Ortiz was 1-1 with a HR would I trade that HR for a double and a double in the 11th or 12th, well no not a chance. I still think more often then not I would take the homerun.
Seems like a good brain teaser with no real answer. Seems like it depends on the situation and many external factors.