Updating the prebinding should not raise issues on your computer since it does not change the contents of preferences or applications files...
I perform this step quite often on my or other Macs and never experienced an issue with it. Therefore, chances are that the crash was related to another issue, already existing before the prebinding was performed...
You may want to perform the other tasks, just in case.
Would you have seen error messages stating that some files could not be prebound, you should not have to worry. Indeed, the update_prebinding command cannot prebind every file on your hard drive — for various reasons.
It is difficult to troubleshoot the issue you are experiencing with so few details. You may however want to remove the X11-related cache and preferences files, in order to make sure that no corrupted file could prevent it from running.
Also, Console messages may be helpful and should give you a good indication of what went wrong.