Personally I would prefer to pay more for a better product, but other users may not want to. Would it be possible to sell two difference Everdrive 64's one with the faster protocol and one with the slower one?
For the $2000 a year for the SD royalties does that mean that for as long as you sell the Everdrive 64's you need to pay that money?
Going on to what Sanni mentioned there is a good chance that someone will do some shifty coding to add in the faster SD protocol anyway. Selling with the slower protocol would still probabally deter potential customers who can't be bothered installing some patch to their cart.