I wonder how Anakin would react to this, or will in fact. Ahsoka just up and disappearing won't really play off on his character.
Apparently Anakin is conflicted by the Altisian Jedi as well. He realizes that if he joined with them he could be open about his relationship with Padme, but ultimately his loyalty to his Clone troopers convinces him to stay with the Jedi. I don't think it is just a matter of her disappearing.