Sorry, but you can't have it both ways. Equal treatment under the law and due process would preclude that.
Actually, the erosion of jury rights came about in part as an effort to assure equal protection. If someone in a community harmed an outsider whom nobody really liked, a jury of his peers may judge him far less harshly than someone who harmed a respected member of the community. I don't really know what the Founders would have thought of that. Allowing communities nearly carte blance to "protect their own" would cause the country to be fragmented into somewhat more isolated communities than is typically now the case, but I would expect that a desire for trade would cause communities to slowly open up. In many other circumstances, free markets are better that forced association at ending discrimination; I'm not sure the same wouldn't eventually have ended up being true here.
In any case, whatever the intention, the invocation of the Fourteenth Amendment to erode the right to be fully tried by one's peers has certainly had some bad effects. I don't know whether it was the best thing to do or not.