It has also been my experience that the opinion of the Michigan Department of Agriculture and Rural Development is that non-rural farming operations should work through local, rather than state regulations. Several things, however, should be noted.
First, this is not the historical opinion of the MDA (as MDARD was previously called). In the years immediately after the 1999 RTF amendment was passed, MDA supported residential farmers who wished to claim RTF protection for their commercial operations. So whether or not folks like us were the main intended beneficiaries of this act, MDA has historically recognized that the act does protect us, so long as our operations are commercial and we follow the GAAMPS.
So the current opinion of MDARD is out of step with the historical opinion of that agency. In addition, it is out of step with the stated law (as I and many others read it), and also out of step with court rulings (most recent case is Forsyth Township v Buchler but there are others), and out of step with how scholars from MSU have interpreted the whole history of the law and court cases. Links to all of those documents are in my post above, and I encourage you to take a look at them.
If you only look at one of those documents, look at the Buchler court case. This was a suit brought by a township against a farmer, to force the farmer to follow local regulations with respect to the keeping of chickens and other animals. The farmer claimed Right to Farm protection and he won. Again, this decision came down very recently, in December of 2012. Not sure how much more clear it can be that the law protects commercial farming operations in Michigan, even in residential areas.
Finally, I would add that most of the folks who you might have talked with at MDARD over this are also not lawyers. I assume you spoke to Wayne Whitman or Jim Johnson? Not lawyers. And if you ask them to justify their opinion that RTF does not cover everyone, I expect that they will be unable to point to a section of the law that supports their view, and will also be unable to provide you with a court decision that supports their view. At least that has been my experience.
However, I do understand that some folks wish to work through their city or township to change their ordinance, rather than claiming RTF protection. That is also a fair approach, and if it is the approach you choose I certainly wish you luck.