Lets also consider lining up karaf feature support more with what's in the osgi subsystem spec. There, a subsystem (including a feature) is a jar with some manifest-like files indicating its contents (and isolation, etc etc). In particular there isn't an idea of a "feature repository" containing several features. I think you can represent a "feature repository" with an obr xml repository document, but I haven't tried.
From this point of view, the problem is that we should be using features rather than feature repositories. Then its pretty clear what to do if you deploy a single feature.