So long as you don't use a soap that has wax or some other coating product in it, you shouldn't have a problem washing a disk brake bike.
I use conventional car wash soap -- rain-X Spot Free is what I'm using now -- and I have never had a problem. I DON'T directly scrub or soap the disk braking surfaces, but I don't take the wheels off or take any other special measures to avoid them. As has been said above, the braking surfaces take care of cleaning themselves. I leave them alone.