This shouldn't cause any problems, but I'd still suggest keeping the usual NRaas mods in place to clean up any stray data. The way it should work is that all sims employed in rabbitholes will lose their jobs and not be given new ones if the game can't find anywhere for them to work. You'll also lose the other activities associated with the rabbitholes, including some opportunities you might want your sims to complete.
It's a good idea to at least leave City Hall intact for its other functions, for example registering as self-employed. But even that's not strictly necessary—you can assign the job with MasterController if you want. And if you'd like your sims to buy eggs and cheese, you'll need a grocery store at least at first. But you can place any rabbithole and delete it again as often as you like.