A friend of mine was denied boarding by Lufthansa many years ago because of a missing "d" in his surname (and hasn't flown with them since!). I believe the mistake was discovered at check-in, though, so there won't have been a note in his PNR.

As a former airline employee I am a bit surprised that your booking agent claims they can't re-issue the ticket without initiating a new booking. Unless their system is radically different from the one I used it should be possible to amend the existing booking (open record - edit name field - save record - print ticket). Have you tried talking to a supervisor?