They will be issuing refunds (Yahoo! will be) to those who have purchased 2.0 or later (although I dont understand what the 'later' means in this context).
I'm sure more details will arise as time goes on as to exactly what will happen with Konfabulator. Arlo has a history of being insanely protective of his work (to the point of not letting people create fansites with his artwork) so I would be willing to speculate that one of the conditions of the purchase revolves around what exactly Yahoo! can do to the app; In terms of bundling their junky toolbar or other misc software, and bundling excessive amounts of Yahoo! related items with the installation in the future.