First of all, thank you very much for taking the time to write, I really do appreciate it! I am deeply sorry to hear that you have been experiencing these issues...
While intensive, the update_prebinding command is unlikely to cause any serious damage by crashing and especially not such broad damage. However, the crash might have been caused by an existing problem that just got revealed by the increased system activity.
You might want to try running the Apple Hardware Test that came with your computer a few times in order to check for potential hardware trouble. Also, you may want to have a look at your hard drive's S.M.A.R.T status, available through Disk Utility.
Let me know if this helps!