Many intentional communities have avoided dealing with permits, zoning and other such local ordinances. Some have successfully operated for a number of years without problems, others have been shut down, red tagged, and had their property made uninhabitable by harassment by local officials. The best advice when you break the rules, is to know the rules well, so you know what your risk is, and what the details that you need to worry about are. One big draw back to getting caught in violation of zoning and building laws is that the local officials may not trust you and therefore they will scrutinize everything you do under the bureaucratic microscope. If your project is the first time the local agency has heard of Cohousing, of coops, or whatever you are, spend some effort to evangelize the idea.
Many groups hire a professional planner or project coordinator to deal with the agencies involved.
Be smart about how you approach agency people and don't ever threaten or yell at them. Find out who can override decisions from lower level employees and lobby those people carefully. The more you can do to sell your project to the local planners, public agencies, etc., the better off you will be. Many of them will be unfamiliar with community and you should educated them with simple, one page materials that lay out the advantages for the agency to this kind of development. If you have the director of the planning department on your side, it makes everyone else down the line on your side.