Have a look at the diagram below:
If hooked up correctly, the positive pole of the battery is connected to the negative poles of the diodes. In this direction, the diodes block current from the battery positive pole to the alternator/ground.
If you reverse the poles, the negative end of the battery connects to the negative poles of the diodes, letting all the battery juice flow through the rectifier. Most of the current will flow through the ground connection of your rectifier back to the battery. This amount of current is far too much for the rectifier diodes. They will die fast.
So the most likely damage is: Burnt wires from battery plus to rectifier and from rectifier ground to battery minus and a fried rectifier.
The alternator should not take any damage, since it does not have a direct ground connection so no current will flow through it with a wrong battery setup.
Also, if you are lucky, the rectifier's ground connection has been in a bad condition (corroded, dirty, etc.) which would limit the damage somewhat...
However, get yourself a multimeter with a diode tester and measure your rectifier's diodes as described in the Honda CB500/550 Workshop Manual...
The rectifier's plug has three yellow wires and one red and green.