I use Gf flours, but sparingly. I try to focus on non-processed foods. Zonulin was only just discovered by Dr. Fasano a decade or so ago. There is no drug or supplement to control it.
Look to other issues that could be causing your problems. Have you researched the AIP diet? (It is strict, but a recent study of of Scripps in San Diego studied the AIP diet with IBD patients who stayed on their meds. They acheived a 70% remission rate. That is amazing!
I do not think GF bread, cupcakes or chips is allowed on that diet! Junk food, gluten free or not, is still junk!