I just take the lighthead off the bike when not in use; put it in a bag or pocket. A rubber cap of some sort would also keep the connector clean. Of course, you could also buy a Y-cable from Geomangear or whomever and use that for charging without dismounting the assembly. Then you could keep the primary connection permanent; even put a heatshrink boot on it.
The other issue is waterproofing the battery assembly. There is a thread about this on BROL, if you search there.