correct me if I'm wrong, but don't the groomsmen wait up by the altar with the groom, and the bms walk up the aisle solo, then you leave the church in pairs?
with that in mind, and the fact that your son is too young to actually walk the aisle alone, my vote is that you hold his hand(s) - whatever he needs to do to make it up the aisle. Personally, I think pics of that are adorable!
Coming back down the aisle at the end, you could just carry him - it's not a 'photo op' on the way out of the church!
Not everyone does it this way....some people choose to have the GM walk the BM's down the aisle....