It was my understanding a player could represent French Guiana (or Martinique, etc.) in a CONCACAF tournament and also represent France. Perhaps it's more complicated in that a player can only go from the overseas department to France and not vice versa?
Malouda helped French Guiana qualify for the Gold Cup and now he's ineligible? This wasn't an issue when Jocelyn Angloma, who had played for France for several years, helped Guadeloupe make the semifinals of the 2007 Gold Cup. The only controversy I remember at the time was that Guadeloupe would not be allowed to compete in the Confederations Cup if they were to win the Gold Cup.
Correction: Malouda didn't play in any of the 6 qualifying matches that got French Guiana to the Caribbean Cup finals, the final 4 teams who also qualify for the Gold Cup, but he did play in that Caribbean Cup. He featured in both their semifinal shootout loss to Jamaica and in their third place win against Martinique.