Keep in mind that disc hubs are MTB hubs pretty much all the time. That means 135mm axle spacing vs 130. That won't be an issue as long as your bike currently has an MTB stle hub in it already.
The 29er wheels all seem to come with slightly wider rims. I just got a set for my own Double Cross build I'm starting on and the rims are Mavic 719's that take tires from 28 to "as wide as will fit the frame". But all the options for brake hubs used these slightly wider rims. The 719's being 580'ish grams each. If you truly want a rim that'll do the smaller road size tires you'll have to have a shop make them up for you. I did a set like that years ago when I made up a Speciallized M4 MTB to be my own foul weather super commuter. Narrow Mavic roadie rims to XT hubs running disc brakes.