I don't feel strongly about smooth scrolling one way or the other, actually, I just hate that it broke that xmodmap hack I've been happily using.
Anyway, let me break the pattern of just complaining. It is possible to have natural scrolling even with GTK+ 3.4, and not just for Synaptics touchpads. Like this:
1. Disable the button remapping hack (comment it out in your .Xmodmap or whatever) -- leaving it there would mean continued confusion.
2. Now, your pointing devices have to support the 'Evdev Wheel Emulation Axes' XInput property. For those that do (I don't have any mice around to check, but my Logitech trackball does, and so do TrackPoints):