RE: batteries with s connectors
The Hitec S, the Airtronics Z, the JR and the Futaba J all use the same wiring polarity with a center pin positive. The Hitec, Airtronics and JR can all be forced on reversed (and the Futaba if the flange is removed). If any of these battery plugs are connected to the typical two conductor switch harness reversed then this will result in an incomplete open circuit, it cannot fry anything.
There is something else happening in your case. Obviously you received one pack with the wrong plug but that in itself will not be a problem (Hitec S plug into a Futaba J switch harness will work fine. Something else is shorted or possibly the plug that fried actually had the pins improperly installed in the plug body i. e. crossed at the factory.
John