Actually, now that I think about it, that is not the source of the problem.
The only way a threading issue can occur is if two commands are run at the same time. But that cannot happen in sublime. Sublime is still effectively single threaded for plugins. Jon more or less has said as much in the forums. In other words, sublime will never allow the cut and paste commands to run at the same time.
Even if my fingers magically instantaneously trigger both commands at the same time, sublime will still have a queue or something to execute one, then the other. Otherwise, EVERY SINGLE plugin would need to be updated to have a lock on their global data, which I know most don't do right now.