President Reagan's recent endorsement of a constitutional amendment that would allow voluntary school prayer has been characterized mainly as a gesture to restless conservatives.

But viewing the president's announcement only as a political story misses much of its significance.

Buried in many reports of the president's statement was the fact that the administration also refused to endorse "New Right" legislation that would strip the federal courts of jurisdiction over school prayer.

By choosing a constitutional amendment, the administration is acknowledging that fundamental constitutional principles must not be sacrificed on the altar of political appeasement.

For three years, some proponents of school prayer have advocated legislation that would strip the Supreme Court and lower federal courts of their jurisdiction to hear school prayer cases.

This bill was seen as a way to address the Supreme Court's 1962-63 school prayer decisions. Such a statute, if passed by a majority of Congress and signed by the president, would free state courts to overturn (or leave alone) previous court rulings on school prayer.

Such legislation presents a radical threat to the Constitution. Since 1803, when the Supreme Court ruled in Marbury v. Madison, the court has determined what is constitutional. Unpopular decisions can be overturned if two- thirds of Congress and three-fourths of the states agree to a constitutional amendment, according to Article V of the Constitution.

The court-stripping legislation before Congress would make an end run around this process.

In his analysis of the court-stripping approach, Attorney General William French Smith stated:

"Congress may not, . . . consistent with the Constitution, make 'exceptions' to Supreme Court jurisdiction which would intrude upon the core functions of the Supreme Court as an independent and equal branch in our system of separation of powers . . . The integrity of our system of federal law depends upon a single court of last resort having a final say on the resolution of federal questions."

I applaud President Reagan and Attorney General Smith for rejecting the court-stripping approach and endorsing a constitutional amendment.

The administration's position is clear: fundamental constitutional values must take precedence over the interests of single-issue groups, whether from the right or left of the political spectrum.

The Senate soon may be asked to vote on the "Human Life Statute," legislation that would overturn the Roe v. Wade abortion decision.

The Reagan administration's analysis of the school prayer issue should be a message to those who support the Human Life Statute. Those in the "New Right" who support the proposed statute should be seeking a constitutional amendment.

There will never be complete agreement on social issues such as abortion, school prayer and busing. But we should agree that Article V of the Constitution provides the framework for us to resolve these public policy disputes.