You'd be fine. Just let the inspectors in and be super-transparent. Plenty of people have research reactors, and if you aren't a belligerent theocracy, you shouldn't have much of a problem. Just play nice.
Micro nuclear reactors don't have weapons grade uranium/plutonium in large quantities, AFAIK at best they could be used to build a dirty bomb. And what would be the point of that ? I'm not proposing building a religious sect, just a society of hand picked individuals from different fields, like engineering, natural sciences, architecture, arts etc.
My undergraduate institution (Reed College) has a student operated nuclear reactor on campus. No weapons grade nuclear material, and it wouldn't make a very good dirty bomb either. However, it's useful for bombarding things with neutrons and it does give off a pretty blue light because of Cherenkov radiation: http://en.wikipedia.org/wiki/Reed_Research_Reactor.
