chesed,
Based on a WSJ report I found (http://www-2.cs.cmu.edu/~dst/Cowen/essays/wj301297.html), the case was the culmination of a long battle where the IRS refused to recognize the Church of Scientology as a real church. Eventually, the IRS relented in 1993.
Based on the report I found, there is no mention of education credits for religious schools. The only “special exemption” I see is where they can deduct costs for auditing — which, in theory, is no different than dedcuting the cost of kibbudim that a person buys in shul.
And, lastly, in any event, the IRS is a federal agency. Education, however, is a state issue. I asked you to provide a cite that Scientologists received credit on their state taxes. You have (so far) failed to do that.
The Wolf