kevinkroon:
Would an externally powered usb hub be a safe option?
Since we don't know exactly what cause the problem, I wouldn't say for sure. If the hub is truly powered from a separate source then that would it would protect the computer from the Arduino somehow forcing a higher voltage on either the power and ground pins for the USB connector.
However, that wouldn't stop a short from a higher than 5 VDC VIN loop or input pin to either of the USB's data lines from reaching the computer. Although this last situation is possible, it seems unlikely given the layout of the Uno's circuitry. If the soldermask was still intact over the traces there just aren't that many places for such a short to occur.