MacBook – How to enable natural scrolling for the trackpad, but disable it for the mouse

There is a workaround, and it is called Scroll Reverser. That screenshot says it all; you can invert scrolling per-axis and per-device.

Lion did change this on you.

Depending on what hardware you have connected, the mouse pane, the magic mouse version of the mouse pane and the trackpad preferences all have a toggle to show if "Natural Scrolling" is enabled or disabled.

If you want your finger moving up on the mouse wheel to move the scroll thumb up (and the document down) just like Snow Leopard, then un-check the box to the left of Move content in the direction of finger movement when scrolling or navigating

If you have other pointing devices (and those reading along at home), hop over to confirm that one setting governs direction on the Mighty Mouse, the Magic Mouse and Trackpad preferences - scroll direction carries over to all input sources.