Yes, the mirror is to big, thats why an EF-s lens could only be attached while the mirror is locked in the "up"-position. The camera would work like an EVIL.
Vignetting wouldn't be that much of a issue as the camera knows the true image circle at a given focal length. You read only the part of the sensor thats actually illuminated. You don't get the full resolution of the APS-H sensor if your at the wide end of lens, but an indicator in the viewfinder could tell you to zoom in a bit for best results.
Similar to the masking the FF Nikons do, but in a more sophisticated way.