I've got a friend who is getting a Bob Jackson built with Disc Brake on the front. They advised against it and said they wouldn't build the forks, but he bought some Bontager ones and they are building the frame around that.
Their reasons were that the frame-building process and subtle geometry would have to change somehow in order to facilitate heavier braking. They did advise him to just buy a Marin, but in the end he convinced them and they did get quite excited about the build. It's due to arrive in the next few weeks!
be sure to post a few pics of it