I would say that there is some chance. Can you see if you are actually getting five volts out of the regulator now? It might have been damaged and if it's wrong then one processing unit might work while the other one won't. It's not good for either one to run it like that.
Probably the only thing that you can do is change the five volt regulator, if it needs it. If you try to replace the ATMEGA8U2-MU chip, while it can be done, you will also have to get the firmware for it and program it before installing it. That's probably more trouble than it's worth. You should be able to program the 2650 chip through the ICSP connector but you won't get the USB back unless you either change the ATMEGA8U2-MU or finagle a USB connection. You could emulate it on the 2650 or connect an adapter.