Admittedly, it's incumbent upon users to double check, but the DRASTIC change from the old theme to the new is really TOO much of a change. As a theme publisher, you really should have created a totally new theme with a different name. Though the new design is lovely in and of itself, with a new name, it also would have likely benefited by not having the old one-star reviews or the support forum issues which are likely to scare new samplers/users of the new theme away.
You're also likely to have even worse problems from users who don't double-check to see the changes/updates and have issues. I'd imagine that many who had the older version may want to go back to the original version 1.2.3.
Though there were a few quirks with the old version (< v1.2.3), it was both lovely and very functional, particularly within the Education space. This new theme doesn't really have any type of educational feel at all and instead seems more like a plain vanilla WP blog format.
For the sake of the community, I honestly hope that you republish the old version under its original name and then republish v2.0 under a new name. If you do this, I'll come back and give the original a 5 star review along with some notes about how to navigate the home page slider that seemed to be one of the bigger issues in the original.