After proper support for the ALIX LEDs got into mainline in 3.3, the ALIX GPIO button support found its way into 3.4. Hoooray! So now it's finally possible to have GPIO + LEDs + button, with vanilla upstream and done the proper way. For this I enabled the input subsystem in the config. So, you should see the button as /dev/input/event0. It generates an EV_KEY with code KEY_RESTART. You can test that with evtest. (Debian package evtest, or get the sources from git://anongit.freedesktop.org/git/evtest.)
Here is the 3.4.0-rc5 config. So far 3.4 is only RC.
If you prefer a more stable version, here is a 3.3.4 config. This config also comes with the input subsystem and polled GPIO enabled, but the GPIO button patch is not included in 3.3. If you want it, apply the patch on top of 3.3.
As always, use these as a working starting point, but you certainly want to fine-tune these to your setup.