The entire bone layers system needs an overhaul.
I think the easiest thing, for now, is to just use the bone layers manager addon. It sounds like your already using it? If not there really is no reason not to use it. Its free and awesome.
You can use that while your weightpainting as well, it won’t disappear. So I think this solves your workflow issue perfectly.
I expect this and more will be looked at for animation 202X.