I linked the actual court decision. No where does it make any statement like the one you have bolded. I'm not sure why you think that author is a more authoritative source than the actual court decision.
Secondly, that statement is ambiguous. Does the author just mean that the court did nor order the church to pay taxes on donations received as a consequence of the ad they ran? Note that the ad called for "tax-exempt donations". That interpretation of your bolded sentence would make sense, given that the ad ran before their 501(c)(3) status was revoked, but it's also irrelevant to the conversation we are having, which is about whether or not the Establishment clause precludes taxation of churches. It's also irrelevant that the church was allowed to re-apply for a tax-exemption.
In fact, the absurdity of your argument should still be apparent in that very statement: if they are immune to paying taxes because of the establishment clause, then why would it ever be necessary to re-apply for a tax exemption? The article also quotes the original judge stating very plainly that the IRS has the power to revoke the tax-exempt status of a church. Again, this is nonsensical if the constitution precludes any taxation of churches. I'm not sure I can make this any clearer.
Sorry, but the straws you're grasping at broke a long time ago.
Nor does the revocation necessarily make the Church liable for the payment of taxes. As the IRS explicitly represented in its brief and reiterated at oral argument, the revocation of the exemption does not convert bona fide donations into income taxable to the Church. See 26 U.S.C. s 102 ("Gross income does not include the value of property acquired by gift....").
https://www.gpo.gov/fdsys/pkg/USCOURTS-caDC-99-05097/pdf/USCOURTS-caDC-99-05097-0.pdf
It also doesn't prohibit churches from opposing legislation or laws. See the lesbian nut job Mayor of Houston's attempt to subpoena a pastor's summons over her degenerate campaign over the Faggot Community's desire to give sicko freaks legal access to molest little girls in women's restrooms as another case that went nowhere re religious rights.
The ruling doesn't say what you want it to say. It in fact does almost nothing except reinforce the guideline that a church organization cannot endorse or oppose specific candidates; it does not restrict a pastor from doing so on his own, i.e. they merely tripped over a technicality, and in no way lost their tax exempt status. In fact the term 'exempt' doesn't apply, since they don't need the IRS's permission to 'exempt' them; the Constitution bars the IRS or any other govt. agency from interfering with them.
If they are primarily a political organization, then they aren't a church in the first place, so they aren't covered by the establishment clause. If they are going to tax churches the way you wish they would, then they would also have to tax political parties and every other charity.
See also
“Congress is not required by the First Amendment to subsidize lobbying.” Regan
v. Taxpayers With Representation, 461 U.S. 540, 546 (1983).
and ...
Cornelius v. NAACP Legal Defense and Ed. Fund, 473 U.S. 788, 800-02 (1985)
If churches were actually banned form
any political activity then the entire Civil Rights Movement and 90% of black churches would have been shut down.
