Where exactly are you having clearance issues?
Disc bikes can be challenging, but not impossible by any means. Here's a pic of how I modified the front stays on my Sojourn to get around the calipers:
http://www.crazyguyonabike.com/revie...ested=0#210535 The back one is handled the same way.
Those are SKS P45 fenders, by the way. I also have installed some Planet Bike fenders on my wife's LHT, and they work fine too - just a bit heavier.