Warhammer Online was an amazing game, in the beta, launch, not so much, but in Fantasy, its easier to make it into an MMO, all the classes there were on the same powerlevel.
40k won't work, because it will have to have marines in it, poster boys of 40k and all that, and realistically, the only grunt trooper of another army that can stand up to a marine, 1 on 1, would be a Chaos Marine, a Necron Trooper (maybe), and maybe some of the Aspect Warriors. If they don't put Marines in, then they'll piss off all the marine fan boys (about 50% of the 40k playerbase, if not more), and it'll be Guard, Tau, Eldar, Nids, etc. We'd get to see all the decent races, but no one would play it. Well not enough to make it profitable at any rate.
The best way to do a 40k MMO imo, would be to base it on Inquisitor, you've got numerous classes, battling against chaos cultists, xenos, everything like that, opportunities for small group based PvP against other Inquisitor Warbands, excellent stories, but it'll never happen unfortunately.