topeak makes rack for disc brakes
Just so you know that topeak makes a rare rack for disc brake mount, which is available from amazon for $19.99.
I have been semi-commuting (good weather, daylight) for about a year now on a WalMart fat-tire. Having decided to try "full"-commuting, I visited my only LBS which only carries Trek, Specialized, and Giant. Looking for a raised handlebar I was put on the Trek 7200/7300 and Giant Cypres, and I felt very comfortable on the Treks. Also tried the Trek 7.2/7.3fx and Specialized Sirrus but didn't like the lower handlebar position. I ended up with an '07 Trek 7300 and put on Freddy hardcore fenders and a topeak explorer rack (regular style); also replaced the stock plastic pedals with a pair of cheap alloy ones with clips and they gave me a skinner Bontrager Race Lux to replace the stock saddle.
Trek 7.3fx has a version with disc brakes but is $100+ more than the regular version. If you like the bike the fenders and racks should not be the deal-stopper.