It costs money to run the App Store, and the majority of apps in the App Store are free and therefore earn Apple no money at all. They are in essence costing Apple money because the $99 a year doesn’t come close to covering the costs of supporting them.
As such, the bulk of their revenue comes from the 30% cut of paid apps (mainly freemium games). Remove that by allowing third party payments, and Apple will need to find a way of still getting money from developers to offset the costs of operating the App Store somehow.
And if Apple can’t get 30% via iTunes billing, then they will just change the name, but either way, it looks like Apple is dead set on claiming what they believe to be rightfully theirs.
And as I suggested in a way earlier thread, Apple could simply have developers sign a revised agreement stating that they owe Apple a percentage of sales regardless, and verify this amount via external audits (which would be way more work for all parties involved).
It’s pretty in line with how I expected Apple to handle the situation.