The column on Sonia Johnson was barely in print when the phone rang and the letters began to arrive. They were variations on a single them: religious bigotry. Each accused me of prejudice against the Mormon Church, which had excommunicated the founder of "Mormons for the ERA."

I admit that I am bigoted against one thing: bigotry. And the church's attitude toward Sonia Johnson smacked of that. But the response was perhaps predictable. When people of one religion or another get enmeshed in politics, and find their politics criticized, many of them instantly react as if their religion were being attacked.

There are Jews in the pro-Isreal lobby who assume that everyone who differs with them is anti-Semitic, and Catholics in the anti-abortion lobby who assume that everyone who criticizes church politics is anti-Catholic. And now many Mormons in the anti-ERA movement are sure that criticism of their own hard line is a sign of anti-Mormon prejudice.

This issue is unlikely to disappear. Right on the heels of Sonia Johnson's excommunication has come heightened convern about another case involving the Mormon Church and the ERA.

In Idaho, Judge Marion Callister, who is a high church official, is hearing a crucial lawsuit against the ERA being brought by the states of Idaho and Arizona and four legislators from Washington State. As federal district court judge, he has been designated to decide whether the extension of the ERA deadline is constitutional and whether a state may vote to rescind its approval of the amendment.

The Mormon Church was in public opposition to the amendment for several years before it excommunicated a member for her pro-ERA activities. In 1977, the church bused 12,000 women to the Utah women's conference where they voted en masse against every article on the National Women's Conference agenda, even world peace.

Since then, missives -- including the one that changed Sonia Johnson's life -- have been regularly read from the Mormon pulpit. In church, in state legislatures and in congressional committees they have made their attitude plain.

If Judge Callister were merely a member of the Mormon Church, it would be inappropriate to criticize his capacity for objectivity. But the fact is that his judge is a church decision-maker, the equivalent of an archbishop in the Catholic Church, several rungs higher than the bishop who excommunicated Sonia Johnson's. He is part of the inner circle that has already passed judgment on the extension and recission issues.

For these reasons, the Justice Department originally asked Callister to disqualify himself from the case. The standard for disqualification, it said, was "whether a reasonalbe person would have a reasonable doubt about the impartiality of the judge." It added that the appearance of impartiality was as important as the fact.

When Callister refused to resign from the case, he said that the church would not influence him. I am sure they would not . . . directly. But if there is one notion reinforced from the excerpts of the new book on the U.S. Supreme Court, "The Brethren" it is that judges are human, products of their own pasts and prejudices, pride and ambition. Can the same man who has been part of one decision for the church have an open mind for the state?

Judge Callister, in self-defense, reminded the Justice Department that he would not have the last word. The question of the ERA would undoubtedly be appealed to a higher court. But the hard-won vote to extend the ERA deadline bought time, nothing else. Judge Callister has the power to use up that time, the entire 1980 legislative session. In a real sense, his would be the final verdict.

The Carter administration, in yet another example of its flabby commitment to women's rights, failed to pursue Callister's disqualification. Now the National Organization for Women is appealing to the circuit court in San Francisco to remove him from the case.

The issue is not religion. I am aware of the fertile American history of intolerance and of the way Mormons were persecuted. I don't think that religious people should be forbidden from taking stands or that a judge's religion is automatically factored into his legal opinion.

But when a judge is also a high member of a religious hierarchy, and when that hierarchy takes a political stand on an issue, and when that issue comes into his court, surely and "reasonable person would have a reasonalbe doubt" about his impartiality. Moreover, it is hypocritical for any religion to play hard-ball politics with one hand and to wrap itself in the cloak of religious immunity with the other.