The Reagan administration's disgraceful attempt to compromise the independence of the United States Civil Rights Commission by firing three members who have been critical of the administration and "packing" it with new members who support his controversial positions, points out how deep the country's moral leadership crisis is today.

It was this crisis that Vernon E. Jordan Jr., former director of the National Urban League and now a partner in a Washington law firm, had in mind when he told an audience that William Bradford Reynolds, the assistant attorney general for civil rights, should resign because he is not supporting the laws of the land.

"If Brad Reynolds' conscience does not allow him to support those things that the nation's chief guardian of civil rights should support, he should resign," Jordon told a high-level civil rights audience this week. "If he insists upon going against the grain of the national will, the laws and the court decisions he is bound to enforce, then he should resign."

There seems to be a similar contradiction between the responsibilities of Clarence Pendleton Jr., the chairman of the Civil Rights Commission and Pendleton's conscience. Pendleton is against busing and affirmative action, views that have made him to most civil rights leaders the "James Watt of the civil rights movement." Like Watt and Reynolds, his is a case of the fox guarding the henhouse.

Although the White House gave no reason for replacing the commission members who have criticized the administration, Pendleton's acceptance, if not approval of the president's decision, is apparent. Those members being replaced have voted against Pendleton because his views don't give him the ability to function as the chief of the commission that has been called the "conscience of civil rights." He should resign.

Pendleton is a conservative who has been the focus of recent articles in USA Today concerning his controversial tenure as chairman of the San Diego Urban League, his high rate of spending commission funds, and his preparing, for $25,000, a pro-nuclear arms pamphlet for minorities. Some of the nation's leading civil rights organizations have called on Congress to investigate Pendleton for his questionable activities.

There are too many questions about him. The man who is to head the commission that is called the "conscience of civil rights" has to be of unquestionable moral integrity.

The commission has to be a watchdog, bipartisan and independent. The other federal agency charged with similar tasks, the Equal Employment Opportunity Commission, is no longer an independent agency but is a part of the administration whose members serve at the pleasure of the president. The Reagan administration already has slapped the EEOC's wrists for daring to defy the Justice Department when it filed a friend of the court brief opposing the department's position in a racial quotas case in New Orleans. That makes the Civil Rights Commission's independence even more important.

But the traditional chorus needs some new voices to stop the president's blatant move to stack the commission. One strategy is to block the confirmation of the nominees in the Senate.

This issue goes beyond civil rights; it is a matter of moral leadership. Where are the nonpartisan leaders of the caliber of the Rev. Theodore Hesburgh, president of Notre Dame University, on this issue? Where is the Rev. Theodore J. Jemison, president of the National Baptist Convention USA, Inc.? At stake here is not politics or party, but the country's dedication to the principles of freedom.

But a first step is for Clarence Pendleton to be replaced. If he wants to spout his controversial views in the privacy of his den, that's fine. But the American people shouldn't be stuck with this bad penny willingly doing the administration's bidding.