Why don't you call COPA airlines directly and ask them? I doub't, however, that you will be able to purchase a ticket - whether for miles or cash - from the US to Cuba, even though you are making an intermediate stop in a third country.
If, however, you are travelling to Cuba with a license from the US government (and by the way, it is NOT illegal for a US citizen to TRAVEL to Cuba, it is illegal to SPEND MONEY there without a license. Many Americans - including Flyertalk members - have legally travelled to Cuba and spent money there), you should be able to buy a ticket from an authorized US travel agent or airline. There are even special charter flights from Miami.
See the US State Dept. travel sheet on Cuba at http://travel.state.gov/cuba.html