Two for one mileage should not be affected by a purchase from a TA. The charge will come from Delta. Airlines have been trying to get the credit card fee to be paid by the travel agent for many years. Go figure why a TA would want to work for free (no commission) AND eat the cc fee. It will happen eventually. It is one of those things that has been bantered around for years in the industry. Kind of like taxing passengers on frequent flyer miles. That too will eventually happen. IMO