Kope is correct, Dorna has already announced new SBK rules that will "dumb down" current SBK spec to be closer to OEM street bike spec. Ducati's brand is absolutely tied to racetrack success so they will do as they have always done and create homologation specials (remember the 888SP, 996R, 1098R, 1198R?) to include every necessary feature to ensure racetrack competitiveness and success.
Regarding price, the 1199R is the least expensive homologation special that Ducati has ever produced. Racetrack success is vital to sales for Ducati, so having a homologation special cost $50,000 (but can win) or more is a trivial concern. They had no problem selling the required number of 1198R's for eligibility in the 2011 racing season (or any special before that), and it will be no problem in the future, irrespective of price (let's say less than $75,000).
I still bet they won't adhere to a twin-cylinder formula. They were able to stay competitive when (Italians) Flammini Group were running SBK as rule breaks tended to fall in their favor, but now with Dorna - a Spanish organization - owning SBK, and being very partial to the Japanese (especially Honda), it is doubtful that the "leveling rules" will ever favor a big twin again. I'll put a gentleman's bet of $1 that by 2016 we will see some type of more-than-2-cylinder Ducati superbike, likely a V4, but who knows what crazy stuff Domenicali will authorize.