I think with the release of the new beta with atom support re-enabled the move to disable atom was one of three things
- A genuine bug, even the mighty Apple isn't infallible
- Apple testing the waters their for technical ability to lockout the platform. Given how little doubt there was associated with that this was deployed and their proclivity to block the Pre and pretty much anyone that doesn't genuflect at the Steve Jobs reflective pool and leave their wallet at the door.
- To gauge backlash and stir the pot. The company thrives largely by capturing mind share, and their lackluster new commercials and a VP promising no new products for the year maybe the shrewed marketers thought of a way to get themselves in the news. If so it worked.