If you put the charge controller chip inside your unit, then you only have to worry about reverse polarity going in to the charge controller (not the battery). This can be handled with a bridge rectifier.

If the charge controller must be outside the unit, then you would need to incorporate a polarity sensors and a couple of relays to connect the appropriate polarity. There is also the problem that the battery may be so flat that you can't determine the polarity. I believe lithium batteries may blow up if reverse charged, so I would be very cautious.