It seems to me that JoeD80 was merely explaining the actual reason behind using the initials, an explanation I have heard myself from other locations. Personally, until I heard that explanation years ago I just thought it was just a little way of having fun more than anything else.
Lots of writers seem to do it -- for example, Douglas Adams/Arthur Dent, Charles Dickens/David Copperfield -- it just seemed to me that JMS was being bloody mindedly persistent in retaining JS as the initials of the station commander.