I'm not aware of any problems with using QR skewers with disc brakes, but having said that one of the first things I do is dump them in favour of allen-key skewers.
Remember uk.rec.cycling?
I'd be lying if I said I didn't ...
A bloke on there, Russ Pinder, broke his back after losing a front wheel from a QR equipped disc braked bike. James Annan wrote an article about a proposed mechanism for such a failure.
That one passed me by, I'm afraid. Given that I went into self-imposed cyber-isolation sometime in the late 90s this isn't really surprising.
As for bolt-on skewers on carbon forks, I ran my old Marin Point Reyes like that for a good 6 years and never had any problems, at least not until the frame decided to crack. Unless you're running Stupid Light[tm] carbon forks I doubt very much that the dropouts will be carbon. Certainly all the carbon forks I've had have had metal dropouts, more than likely alloy.
My preference for bolt-on skewers is more from a security standpoint than anything else, having learnt the lesson the hard way when I worked at York Uni - some scrotes managed to get into the locked cycle cage behind the Electronics department and pinched the skewers out of the wheels of my (then) Audax bike; clearly they planned to come back for the rest later.