"If the people involved in this were Amish, instead of Orthodox Jews, would the zoning board have ruled differently? "

You can't use hypothetical questions because there are no real answers.   I would say that in this case, the answer would be that the outcome would be the same if the issue involved the Amish. However, those opposed would say that the Amish would get preferrential treatment. There is no right answer because the question is not valid.   

I'm sorry, but I also do not think that bringing up Jim Crow laws are applicable in this case.   There is no denial of basic human rights and the laws, from what I have read so far, have not been changed to descriminate. The laws are what they are. If you feel that laws are unjust, you work to change them - but be prepared because others think the laws are fair. That doesn't mean "discrimination" - it is just that there are other opinions and concerns.