Please understand that these men were not necessarily fighting for slavery. Probably none of them were slave owners. They were fighting for the right of their state to make that decision instead of the Federal government! they fought for states rights. It just got wrapped up in slavery because that was the issue du jour. If slavery had been abolished earlier than the 1860's, as it almost was in Virginia before the invention of the cotton gin, then they would have been fighting over another issue.Either way, those men fought and died for their state, not the right to own slaves. As such the conditions of their funeral should be dictated by that.
Of course this is all moot. Didn't someone already point out that they were not military? Wasn't the Hunley a privateer working under a Letter of Marque?