In October 1993, during the first year of the Clinton administration, Scientology received its disputed status as a tax-exempt church. In the years leading up to that, thousands of Scientologists had sued the I.R.S., claiming discrimination after the government began to audit their tax returns.

I remember a PR firm Hill and Knowlton had been hired to help Scientology through the previous year.

Shouldn't the trend have been the opposite direction, with "churches" like Scientology and Mormonism losing their tax exempt status, not gaining it?

I doubt that it will be removed completely. What I see is more of a hybrid where the entity claiming the exempt status will have to account for dollars that are not used for the benefit of members, and the general welfare of the community.