Pastor Rick Warren of Saddleback Community Church is fighting for an important constitutional principle that keeps the state from harassing churches. Most churches designate a portion of their clergy compensation as a "parsonage allowance," which is sheltered from federal income tax (although it is taxed for Social Security purposes).

Like 850,000 other clergy, Warren uses the parsonage allowance exclusion. A few years ago, the IRS had a bone to pick with this high-profile Southern California pastor. Warren said he should be able to shelter the amount he actually paid for the housing in his upscale community. The IRS said he should exclude only the fair market value of his housing. Further, Warren disputed the fairness of the fair market value assessed by one IRS agent.

But after the two sides went to court, and an appeal landed in San Francisco's 9th Circuit, they found themselves jointly defending one point: the constitutionality of the parsonage allowance exclusion. Is the parsonage allowance constitutional? The court suggests it isn't, arguing that Congress is "establishing religion" by granting this benefit only to clergy.

Give us a break. The First Amendment prohibits Congress from playing favorites among religions, and it was drafted primarily to protect religion from government interference. A tax break that neutrally benefits all clergy of all religions is not "an establishment of religion"—a phrase that had very specific meaning in its 18th-century context, when many colonies still had religious requirements for voters and taxes that supported a favored church.

In the current context, the issues are twofold: judicial trespassing on legislative turf, and the impediment to America's churches. Congress is empowered, not ...