Meh, that's kind of the point, no? Seems like it would be more jarring to only federate at the community level, as you either a) still have to interact with people from the unwanted instance or b) deal with randomly hidden comments from that instance. If the community dies because it's on an unpopular instance, well, that's the way it goes. Can always start up/join a community on another instance that's federated with yours.