In this case, two girls were kicked out of a "Christian" school for allegedly being lesbians! "The school is owned by the Wisconsin Evangelical Lutheran Synod, the nation's third-largest Lutheran church body. The California Lutheran High School Association, comprising three dozen churches and religious schools, operates the campus."
John McKay, the school's attorney said, "You can't infringe upon the basic rights of a religious group and their right of association by forcing them to accept people who don't believe in their values."
That statement supports my argument! If a religious organization is akin to any private club or organization that can select those they want as members, then they should be treated no differently than those other private clubs or organizations that do pay taxes.
Even if churches and church-run organizations weren't discriminatory, I'd still advocate for their taxation!
The Church's mandate in this world is to be an agent of God's love, and preach and seek to live out the Gospel of grace! As practiced in fact, it is usually little more than an arm of the State, largely condoning, fostering, and ignoring the discrimination against, and the oppression of, others; practicing the politics of exclusion in the name of God; rarely dealing with corporate and State initiated and approved sins but, rather, dealing with personal sins that serve to inculcate insufferable guilt upon others as well as help bring more money into their coffers.
Moreover, if they can't make money judging other people's sins (something Jesus forbids us to do), such as divorce and re-marriage that Jesus condemned (save for reasons of fornication--Matthew 5:32), as probably about half their congregations are made up of such people, they choose issues that are not sins and label them as sins to continue their false religion of exclusion and even hate and receive tax exemption for so doing.
It is inconceivable how any Christian can exclude others from fellowship, and engage in discriminatory and judgmental rhetoric and behaviors that Jesus precisely told us not to do! (Matthew 7:3)
And we're going to continue to allow such organizations to be exempt from paying taxes?