A "class mod" would necessitate custom made maps for the purpose. Notice how in JA Siege it wasn't just a class mod that could be applied over the top of FFA in the normal maps. Instead you had custom maps, with goals and specific objectives for each side. The classes were balanced for the scenario, rather than across the board.
I figure the same thing would be applied here. The main reason you'd think classes would be good would be in a team based scenario, perhaps with the revive command and doors you have to slice/demolish and other such tasks. Simply having CTF and people with different starting weapons probably wouldn't work too well, unless you radically modified how the weapons behaved, and got rid of weapon pickups.
If you want to see how classes could work in RC, just look at any other FPS game that has classes that works, and see what approach they use. I agree applying classes over the top of the current game probably wouldn't be very good. This approach is certainly a lot more work, but it would in the end be much better I think.