Guantanamo is not a major import harbor for Cuba. Morro Castle is a more analogous example. It commands the entrance to Havana harbor, and would have been a real problem if they had wanted to stop shipping into Havana.
The Cubans would have never agreed to a permanent presences of foreign troops in Morrow Castle. No sane nation would ever agree to foreign troops continuously occupying the entrance to one of it's most important harbors.
It wasn't that major of a port for the South. New Orleans, Mobile, and Savannah were all busier in terms of exports or imports. Charleston was an excuse for Davis to start his war, nothing more.
Neither was Charleston Harbor to the Confederacy, as DoodleDawg so well pointed out in Post #487 or 489 above.