What are some good methods for adding charging control/signaling for a docking wireless system with a rechargeable battery?
While a control signal might sound nice at first, I think you'd be better off with adding current limiting to the docking station as your fail-safe.  Here's why:


Limits the charge current to the wireless device.  While your wireless device probably already has some sort of battery charging circuitry, it doesn't hurt to also limit it on the docking station.
This inherently buys you the protection you seek.  If someone drops something that would normally short out your power supply, your docking station is now actively limiting current to a point where no damage occurs to the dock.  Sure, it's technically shorted if you have a paper clip across the terminals, but if you properly limited the output, your power supply will happily be supplying current and all you'll end up with is a warm paperclip instead of a fried docking station.


A step up from this could be that you have an output LED to indicate a charging fault.  Based on the assumption you have current rate limiting for charging on the device side, you could program your host device to turn off the power if the current limit goes over the normal rate of consumption you'd see from the wireless device.  The LED could then be turned on to indicate a fault, in this case, a short circuit across the 5V and ground terminals.

A step up even further could be some sort of momentary switch that got actuated when the device was sitting firmly in the docking station.  That, in addition to the current limiting, would be a pretty sure-fire way to ensure that you weren't supplying power when you shouldn't be, but also that if you were supplying current, it would be safely limited to prevent the docking station from overheating or frying itself.

Ultimately, pulling out another signal as a separate pin offers more of a chance to short something and would still require adequate design to make sure that shorting the control pin to ground, or another pin, didn't fudge anything.  As you said, it's all pretty low voltage but in my eyes making the device handle the fault condition gracefully is better than relying on another condition that is just as error-prone.