Okay, it really bugs me when I'm looking at themes that the Ubuntu icon comes back, so I decided that I'd look at scripting a "fix icon theme" script. I know it's fixed in mintmenu 3.1 but I guess there's other things that will look for start-here.png and novell.png etc. so it may retain usefulness to fix here anyway.
Guess what, it worked! If only text attachments worked in phpBB I'd be able to post it here... and my mintupload isn't working either, *sigh*, http://www.bikerwitch.org.uk/files/mintify-icon-theme.sh
Steps to use :
Download my script above and save somewhere you know where it is (/tmp/ or your home directory is good)
Open up "Appearance" from the Control Center or Preferences in the MintMenu
Drag your icon theme straight from firefox into the window (or download and install etc.)
Apply a theme other than the theme you want fixing and exit Appearance
Open a terminal and run the script mintify-icon-theme.sh themename (you may need sh before if you don't know how to make the script executable)
Re-open "Appearance" and viola, selecting the theme will maintain your mint logo!
What the script does :
Looks at the "Cassandra" icon set that is on Daryna also, copies the .png files to the same place in the user's theme and edits the theme index file to include any missing directory definitions (yes, most themes have wildly different indexes to what is really there!)
I hope this helps someone. Oh, and it's GPL/BSD/Copyleft/Any other reasonable license multi-licensed.