David, you can have your OEM shock rebuilt. There are a number of shops that will rebuild and re-valve/tailor an OEM shock. This is probably the most cost effective approach, and you can even have the shop dial-in the shock for your body weight/height and riding style/venue at Burundi.
With any dirt or dual-sport OEM shock, there is the impulse to replace the unit or condemn its function. Assuming the original shock is not damaged, and yours is in this case, it really pays to follow the factory guidelines for adjusting the OEM shock. Most often, you can find the ride, dampening, rebound and sag that work best for your riding—all within the range of the OEM shock adjustments and fluid choices. We do this with auto/truck seats and suspension/shocks all the time, it's the same with adjustable OEM motorcycle shocks and forks.
As for shock rebuilders, you may even find an "exchange" unit or take-off OEM shock. Whether you want a premier source for parts to rebuild the rear shock yourself or plan to sublet the unit for rebuilding, I suggest that you begin with Race Tech. Here is the page for the Honda XR650R offerings, both parts and labor, for the front forks and the rear shock/spring (scroll down the listing). I plugged in the 2001 model year, presumably 2000-2007 Honda XR650Rs are virtually the same:
Trust this helps. There are also other mail-order sources online for seals and rebuild kits if you don't want to ship the rear shock to the U.S.A. Might want to disassemble the OEM shock (by the book, please, don't turn a spring loose at your home garage!) and inspect the damage. This could be just a seal problem if the tolerances are still okay with no scoring. If you need info on safe disassembly and rebuilding, just ask.