Some coaches shy away from protocols in general because of their association with restriction which some practitioners and coaches deem to be psychologically unhealthy. The "Anti-Diet" movement has fostered the belief that restriction is BAD. While unhealthy restriction of calories and shame induced behavior is toxic, restrictions in the pretense of protocols aren't necessarily in the same pool.
The difference between Gut Protocols and Diets are pretty obvious once you dig in. Diets are generally labels given to a set of eating principals adopted in order to achieve a desired outcome (usually weight loss) and can take many forms. If you look up all of the diets that have been thrown around over the years, it's fairly curious. Everything from Maple Syrup Diets to No Fat to obscene amounts of one or two foods only. THAT ISN'T HEALTHY>
A protocol, especially a Gut Protocol will generally consist of an elimination process, removing multiple foods and even entire food groups for a temporary or long-term basis. A protocol should be put in place with the intention not just to "lose weight" but to irradicate troublesome symptoms, strengthen the body, achieve better health, mobility and less dependency on pharmaceutical support. The intention is the strongest difference, second to the process. If the process doesn't consist of adequate nutrition, diversity, calories and fuel, then it's not supporting your health, it's manipulating a desired outcome. Any protocol should support the health of the vessel and improve the ecology of the gut microbiome and its influence over the many aspects of human wellness.