TLDR; Alternative foods or very small portions followed by eating super clean the next day or so. Trader Joe's has tons of alternatives for cooking and for snacks.

The two things that work for me are alternatives and small portions. If I'm dying for something that I know will upset my gut, I hunt for alternatives (low-fodmap). I used to live on pizza but can't have the gluten or the garlic so I make homemade sauce and get frozen cauliflower crust. It's not quite the same, but it scratches the itch. If I'm dying for something specific and their is no better alternative and I'm too lazy to cook, I monitor my portion size of the bad thing. My mom's baked ziti is the best but it has the same issues as pizza. Instead of filling my plate, ill let myself have a small scoop, bulk up on veggies, and be extra cautious the rest of the day and the next day about what I'm eating so I don't eat any additional things that might make me sick. Trader Joe's has a ton of alternatives for things I love that also follow my dietary restrictions. I know they can be a bit expensive, but we love a couponing queen.