Ed W wrote;
If I'm happy to edit the database can someone talk me through which tables reference the user table and how safe it is to delete these if they have never made any real edits to any content
I had a similar problem, at one point I had ~250 'real' users and ~250 'bot-fakes. Not sure what the 'bot created users were about, but they seemed to have come in three waves with a decreasing number of fake users created per wave. I excised all of the 'bot created users from my database about two weeks ago and have had no new ones created since. I'll try and go over the steps I took to excise the fakes, but please keep in mind that A) I didn't write things down, so I might forget something, B) I know diddly about SQL, C)I know diddly about MediaWiki, D) It is never, ever, ever a good idea to follow my advice on anything. Oh, and make sure you back up your database before doing anything. Maybe back it up twice. Or maybe three times. Just in case.
1) Using phpMyAdmin I went into the user table and deleted all of the fake users (hit browse, check the ones you want gone, hit delete).
2) Some users had signed up during and after the waves of bot created phonies. I renumbered the user_ids of these users to make things consecutive again, being careful to make a list of 'before' and 'after' numbers.
3) I changed the user_id auto_increment to new highest user_id number +1.
4) I went into the user_rights table and deleted all entries past the new highest user_id number.
5) I went into the watchlist and checked to see if there were any entries with a user_id that had been changed and updated those (id est, if I had changed user_id 428 to 250 in the user table, I changed it in watchlist if there was an entry for that user_id).
6) Two of the users with a changed user_id number had done editing on the wiki, so I went through and searched tables that seemed likely (ignoring tables like brokenlinks, categorylinks, hitcounter, and others that seemed unlikely to have user entries or data in them) for those user_ids, changing them where they appeared to the updated user_id.
While something of a PITA, it was easier to do than I expected. The 'bot created users are gone from my database and everything seems to be running fine.
I hope that's of some help.
Myria