My understanding of the law, the court system, and your particular case is really thin, shadygrove, but I am going to suggest that your court case didn't test this particular question - whether or not MDARD is required by law to conduct a GAAMPS inspection for a farming operation claiming RTF protection when sued for violation of local regulations. That language from Section 4 of the law looks clear and unambiguous to me, and suggests that MDARD actually is required to undertake an inspection of farming operations for complaints of any kind.
I don't think anyone being sued for zoning/ordinance violations has requested a GAAMPS inspection by right of Section 4 subsection 1 of the Right to Farm Act, so we don't know how MDARD would respond. Is that correct, shadygrove, or is that an argument you explicitly made to MDARD? In any case, I am just suggesting that in addition to the MAEAP option for becoming GAAMPS compliant, it is possible that Section 4 could be used to get a GAAMPS inspection for folks currently being sued.
Here is Section 4 subsection 1 again, followed by subsection 3 (which describes how MDARD is required help you become GAAMPS compliant if you aren't already compliant at the first inspection).
Sec. 4. (1) Subject to subsection (2), the director shall investigate all complaints involving a farm or farm operation, including, but not limited to, complaints involving the use of manure and other nutrients, agricultural waste products, dust, noise, odor, fumes, air pollution, surface water or groundwater pollution, food and agricultural processing by-products, care of farm animals and pest infestations. Within 7 business days of receipt of the complaint, the director shall conduct an on-site inspection of the farm or farm operation. The director shall notify, in writing, the city, village, or township and the county in which the farm or farm operation is located of the complaint.
(3) If the director finds upon investigation under subsection (1) that the person responsible for a farm or farm operation is using generally accepted agricultural and management practices, the director shall notify, in writing, that person, the complainant, and the city, village, or township and the county in which the farm or farm operation is located of this finding. If the director identifies that the source or potential sources of the problem were caused by the use of other than generally accepted agricultural and management practices, the director shall advise the person responsible for the farm or farm operation that necessary changes should be made to resolve or abate the problem and to conform with generally accepted agricultural and management practices and that if those changes cannot be implemented within 30 days, the person responsible for the farm or farm operation shall submit to the director an implementation plan including a schedule for completion of the necessary changes. When the director conducts a follow-up on-site inspection to verify whether those changes have been implemented, the director shall notify, in writing, the city, village, or township and the county in which the farm or farm operation is located of the time and date of the follow-up on-site inspection and shall allow a representative of the city, village, or township and the county to be present during the follow-up on-site inspection. If the changes have been implemented, the director shall notify, in writing, the person responsible for the farm or farm operation, the complainant, and the city, village, or township and the county in which the farm or farm operation is located of this determination. If the changes have not been implemented, the director shall notify, in writing, the complainant and the city, village, or township and the county in which the farm or farm operation is located that the changes have not been implemented and whether a plan for implementation has been submitted. Upon request, the director shall provide a copy of the implementation plan to the city, village, or township and the county in which the farm or farm operation is located.