Just to clarify 5twins statement Yamaha never put a spoke wheel with a disc on the rear of the XS650.
Being as you have a hard tail it well be easier to swap in some other brand of spoke wheel that did use a disc brake.
A lot of people mod a Harley or Harley clone wheel to a hard tailed XS650.
On a hard tail you are going to have to add tabs and mounts and such to use either brake.
So it's your choice on them.
I have ridden my 75 with the stock 18 inch drum rear wheel and a mag disc brake wheel. As far as how they work, both work well. A drum brake takes more input pressure on the pedal to get the same braking action as a disc brake.
IMHO the ease of pedal pushing make the disc easier to feel the braking action and a bit easier to modulate the brake.
Others may have other opinions.
Leo