If the batteries are empty when connected?
I can't say I have never seen a completely discharged battery and my experience is limited when it comes to lithium cells, BUT most batteries will have some charge remaining, even after heavy use. So, is that really a problem? Just asking.
As for the original question and the challenge of making it idiot proof, the real problem seems to be that the current flows one way when using the batteries and in the opposite way when charging them. I am assuming that the battery packs are removed from the model airplane for charging. That would allow flying with one battery while charging another.
SO, I believe I have seen NiCad batteries that had one connection for use and a separate connection for charging. Both were built into the same connector for a minimum parts count, but they used different pins. This suggests that a simple, three pin connector could be used. One pin for common or negative, I guess, and then a positive pin with a direct connection for use and a second, positive pin with a diode for charging.
So in use current flows out the first positive pin with nothing to interfere. You get maximum power - no Voltage loss in a diode or other circuit. And when charging the second connection is used and the current can only flow one way, the correct way, with the steering diode.
I looked at some RC batteries and they seem to come with a variety of connectors. Most already have two connectors and perhaps one of them could be repurposed as the charging connection with a different pin arrangement. But the charger would also need to be modified. Perhaps it would be easier to modify the connector for actual use of the battery, perhaps with a three pin, omitting the center contact.
Another thought would be to epoxy the two connectors together, but staggered. The one sticking out the most would have the steering diode added and it would be used for charging. No modification to the charger would be needed. The one that is set back some distance could not be physically plugged into a connection on the charger but a cable in the airplane would easily reach it. It would have no diode and would be used for actual flying.
If both of the original connectors are needed while flying, then a third connector for charging could be added, probably to one pair of wires and with the steering diode. The two original connectors would be attached on two sides of the charging connector and both would be staggered to the rear to prevent them from being plugged into the charger.
Put a (fat) diode across the mosfets which conducts when the polarity is reversed. Make sure there is a fuse in the path to the batteries though.
That would do the job,
IF the battery is charged when connected the wrong way.
But the challenge remains, if the batteries are empty when connected.