>The Law of the Land cannot give special dispensation for certain religious groups.
Not that clear cut. Start with, "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof..." and extend it by state constitutions with similiar language, statutes, and case laws.
In general that means that government regulations are not extended to religous organizations, if it conflicts with the self declared religious principles, unless there is a compelling public safety purpose.
So Planning & Zoning regulations and architectual style codes do not apply to churches and associated buildings, building codes do. A city can't tell a church where they may build a church or how big it is or what materials are used to side it, but they can tell them how to build it so it doesn't fall down in an earthquake or trap occupants if it catches on fire.
Perhaps the most tangible aspect is the tax exemptions enjoyed on most church income and property. It's not that government exempts them because they consider them useful social institutions (indeed, such a finding would likely place it in conflict with the 1st), but they are exempted since taxation represents undue influence and control by government beyond the needs of public safety on a religous establishment.
There are a myriad of other exemptions provided based on sincere religous beliefs. Concientious objector status from military service and (many state's) exempting mandatory school attendance till the age of 16 (allowing instead formal education to end at the 8th grade, about 13) are two the Amish enjoy. Exemption from the Social Security Insurance system is yet another religous based "perk" for the Amish.
There are few if any "Class 1" Amish dairies, Class 1 being those that produce fluid milk to be marketed for human consumption. That's due to public safety requirements of how to milk, clean equipment, and store milk. There are many Class 2 dairies which serve the cheese producing market and have lower sanitary standards, but even here many of the more conservative Amish are finding tightening regulations more then they're willing to accept.
In this whole context, a specific technology like RFIDs could be given an exemption provided a reasonable alternative (metal ear tags) meet the public safety needs.
There is a larger issue with NAIS, which is it is simply security theater. The problem with infectious animal diseases, particularly their economic impact, is largely borne by industrialized farms. We've been controlling diseases like TB and Foot & Mouth quite nicely using paperwork for decades.
Instead of asking the fundamental question whether single dairies should have 1000 head of cattle under one roof or a beef feed lot should have tens of thousands of head of cattle wallowing in their own filth for months on end, the USDA decides the solution to the problem is better tracking. No, the solution is diversifying and deintensifying the farms -- yes, it has an economic impact that our food might cost marginally a bit more. It would also mean an system fundamentally less vulnerable to disease, weather, and attacks; if we paid the same share of our income for food as we did in 1970 we'd probably eat much healthier and we would have the mythical American family farm actually doing quite well financially -- any farmer of ordinary ability could enjoy a middle class income. Instead we have overly industrialized processes more vulnerable to diseases and other risks along with negative rural social policy impacts, and instead of addressing this sucking chest wound the USDA in bureaucratic fashion is telling people they have to wear oxygen masks to compensate.
I'm no birken stock wearing slow food maven. But there is a happy middle ground between over concentrated, over industrialized owned or controlled by relatively few corporations and some hippy vision of organic farms with cows who willingly sacrifce themselves to their benovolent master's needs. NAIS is just useless window dressing.