The credit card companies won't allow a merchant to offer two different payment options side-by-side, without charging the same fee. I wish this wasn't the case, but unfortunately we have to abide by their rules. To allow your owners to pay for free via e-check, you can change your payment setting (from your League Settings tab on the league home page) back and forth between the two options.
So, you'd switch it over to the E-check Only method for a day or two; let your league members know they can pay for free via e-check during that time; then switch it back to the Credit Card (flexible) option; and allow everyone else who wants to pay via credit/debit card to do so at that time.