Apple has done the right things. Perhaps some history will help to explain this.
The old scroll behavior was based on the scroll behavior of a mouse wheel. You turn the top of the mouse wheel in the direction you want the document to go.
Seven years ago, Apple introduced the iPhone. This is important because it trained people to scroll pages the natural way, like in the real world. You directly push the object in the direction you want it (the page) to go, not the user interface device (scroll wheel).
Apple realized there was now an inconsistency between the real world (direct manipulation) and the way that scrolling had worked for years since scroll wheel mice were invented for Windows and then used on Macs. Apple decided that the inconsistency should be resolved in favor of the real world, as the iPhone had done. You push the thing you want to move. Direct manipulation.
This is why the new default behavior of scrolling is called natural. Because it really is natural.
I realize it is "backwards" to what you are used to, but I hope the above shows that in reality, the "traditional" way of scrolling was actually backwards and in contradiction to how direct manipulation should work. The old way was wrong. Apple has fixed it, and we have gesture UIs introduced by the iPhone to thank for this worthwhile correction.
It will be a pain in the rear for a while, but stick to the new setting and you'll soon be as used to it as you were to the old, backwards way.