I recently bought a set of Blackwell Research carbon clincher 50s with Campagnolo hub for $1000. Couldn't pass that up, right? Well, I just bought a new TT bike with SRAM Red drivetrain. Would it be worth it to have the wheels rebuilt or just sell them and get new race wheels?
Well, if you can get resell them for that price and pick up a compareable set with Shimano rotor for that money it would be the hassle free option. Question: is it really a Campagnolo hub or some other brand with a Campa rotor? You can swap the rotor on some hubs.
Personally I'd try that first and then rebuild (probably with a nice DT hub...) but I can build bike wheels.