The smart and fair thing to do would be to remove tax exemption for all religions.
Who are any of us to say Scientology is "not a religion"? Of course it is.
I think there is a good reason to keep churches tax exempt, because it maintains separation of church and state. The law currently is that these churches cannot promote politicians, although its poorly enforced. If churches are taxed, then politics would become inseparable from religion. Keep the separation of church and state, keep churches out of business activity (or tax it as such), and keep churches out of politics.
But about Scientology: nobody in there considers this a religion, its an "applied philosophy" all about pumping up your ego. They only give a "shore story" about them being a region for tax exempt purpose. All of Scientology is a "shore story", Hubbard was a liar and a crank. But its a great story on the importance of family and the love that goes with that, because its completely absent in Scientology. Taxation is difficult because legal definition of religion.