This is an amazingly frustrating problem I have also encountered and attempted to solve. I shut off Itunes Match and that allowed me the menu option in itunes of shutting off genius. After those steps, there were no genius playlists remaining in itunes, but even after synching the ipad, they remained (duplicated no less!) on my ipad. Also, as part of the above attempt, I shut off itunes match on my ipad as well.
Now, I thought i had a solution after leaving the above settings and then removing all synching of music within itunes (uncheck the settings for synching music under summary, also uncheck synch music box under music for the ipad when listed under devices on itunes). Itunes then showed me with no music within capacity on the summary tab, however even after synching (and turning the ipad on/off and synching again), the music and those genius playlists remained (clogging up) the ipad.
Unbelievable.
I have not tried a restore yet (previously suggested) but that appears the only remaining option.
Please, anyone, advise if you have an idea that works.