There are certainly a lot of gut-connections with the brain in a lot of ways. reading GAPS was really eye-opening for me as well. And going through GAPS with DH, the change in him emotionally has also been surprising. It isn't all "in his head."
For me, though, I can only speak from my own experience. When I went vegan, I was able to get myself off of a lot of chemicals in processed foods. That made a huge difference. It was like going through withdrawal.
Changing to primal didn't do much, but changing to this IF protocol has changed a lot of things too -- such that I'm way more sensitive to "off diet" things (immediate reactions in the body).
But, this is still my primary process, and until I was willing to be really direct with myself as an emotional eater in this way (not that other ways aren't also helpful, but simply "it's ok, move on" certainly isn't helpful for me because it's a good place to "hide"), I wasn't able to really know that I had power over it.
It isn't just your gut making you do it, though I grant, that it might not just be your mind that gets you through/out of it.