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For years, the focus on the separation of church and state has been on how to keep the church out of the state, not the other way around. But here are three examples of the need to keep the state out of the churches.

Much has been made about the importance of keeping church and state separate — such as the dozens of lawsuits over the years from civil libertarians to keep Nativity scenes or the Ten Commandments as far from government property as possible.

Almost invariably, the focus in such controversy has been on how to keep the church out of the state, not the other way around.

Until now.

It seems now the focus needs to be keeping the state — or more specifically, state and local governments — out of the churches.

Consider these recent cases in point:

In Houston, five Christian pastors were served with subpoenas by city prosecutors to turn over emails and transcripts of sermons addressing homosexuality.

The city earlier this year passed the Houston Equal Rights Ordinance, providing broad anti-discrimination protections to gay and transgendered residents. Both a lawsuit and a petition gathering signatures to repeal the law ensued, and the pastors — who weren’t involved in the lawsuit but did support the signature drive — were issued subpoenas, with Houston Mayor Annise Parker tweeting the emails and sermon transcripts were “fair game.”

In Coeur d’Alene, Idaho, the owners of the Hitching Post Wedding Chapel were told their refusal to perform same-sex weddings violated the city’s non-discrimination ordinance.

Warren Wilson, the city attorney, told an Idaho paper that the chapel “would probably be considered a place of public accommodation” and would therefore “be subject to the ordinance.” This is in spite of the facts the chapel is registered as a “religious corporation” with the state and the stated mission of the owners — a husband and wife who are both ordained Pentecostal ministers — is to perform “one-man-one-woman marriages as defined by the Holy Bible.”

In California, elective abortion is now deemed part of “basic health services” that all insurance plans must cover — including the plans bought and provided by churches for their clergy and staff.

This all comes from regulatory changes, as the state’s Department of Managed Health Care — prompted by the American Civil Liberties Union — has re-interpreted a four-decade-old state law on health services covered by insurance, now ordering abortion be covered by all plans. Ironically, California’s DMHC — along with the U.S. Department of Health and Human Services — exempt churches from any contraceptive mandates, yet they’ve now issued a no-exception abortion mandate.

It’s disappointing, but not surprising, that many of the same groups and individuals who protest even the slightest religious acknowledgement in public affairs are silent with regard toward these unwelcome intrusions of the state into church matters. Many are unsympathetic to religious stances to same-sex marriage, homosexuality and abortion, given that all three are becoming increasingly accepted in secular society. But even though all may have won several sizable legal battles both here and abroad, the practices remain contradictory to doctrines and principles of many of the world’s most prominent religions.

In theory, those religious principles and practices are protected by the First Amendment. In reality, however, protections for religious conscience are proving to be woefully inadequate. The presumption seems to be that the free exercise of religion is only acceptable if it can justify itself in the eyes of the state. That’s contrary to both the letter and spirit of the U.S. Constitution.

We recognize the importance of keeping government from being dominated by religion, but the threat today is not creeping theocracy, but rather government insertion into private matters of religious faith. The First Amendment that was written to prevent the “establishment of religion” also forbids “prohibiting the free exercise thereof.” If that doesn’t protect matters of conscience unpopular with the day’s latest trends and causes, then those words have no meaning.