I'm certainly not suggesting undoing the serum would put Cap on a level where he'd get beaten up by random street toughs, but certainly on a level Batman can handle.
We have seen Batman devise cures for mutations before (I'm thinking of Man-Bat specifically, and I have the impression he's done it for one-shot villains, but I can't think of any examples off the top of my head). Why not for his recurrent rogue gallery? Because they're his recurrent rogue gallery.
Has it really not happened before? Getting depowered by the forces of Evil, saving the day anyway, and somehow getting your powers back is practically a requisite for powered heroes. I bet there's a tvtropes page on it, but I'm not going looking for it, and I wouldn't be cruel enough to link it if I did find it.
....And I went searching for it anyway and it's now 2 hours later and I don't know if I had any more points.