At his first presidential news conference two years ago, Ronald Reagan scandalized some centers of fashionable opinion by suggesting that national moralities matter, and that the Soviet Union's is not to be found in the Boy Scout Handbook.

It happened again last week when the president repeated the message before the National Association of Evangelicals. He extolled the Judeo-Christian roots of political freedom, and unabashedly proclaimed their superiority, as he sees it, to the secularist values of Soviet doctrine.

The reaction suggests that Reagan is taking too seriously Theodore Roosevelt's notion that the presidency is a "bully pulpit." Please, Mr. President, not that kind of pulpit!

If I understand them, the president's critics lodge two somewhat contradictory objections. One is that since the evangelical Christians are presumed to be a Reagan constituency, the president was merely juicing them up for political purposes.

The other is that surely no contemporary president can really believe--can he?--that the East-West confrontation is some sort of Armageddon in which we battle for the Lord and they--the Soviets--for the hosts of Darkness. Not, protest the critics, in this "multi-polar" world where few issues, from nuclear weapons to commodity prices, have a clear theological dimension.

Both interpretations, one imputing cynicism and the other imputing a bumptious naivet,e, cannot be on the mark. Neither may be. What if Reagan really believes what he said in Orlando, and believes it needs saying? Now, that would be something, wouldn't it?

One problem is that the press reports such speeches in snippets, stressing provocative passages. It is true that the president complacently cited a recent survey that "concluded that Americans were far more religious than the peoples of other nations." Religious fervor capable of being elicited by surveys is likely to be the fervor of the self-satisfied Pharisee.

But the president was not, as some of his critics seem to gather, dividing the world simplemindedly between light and darkness. "Our nation, too," he said, "has a legacy of evil with which it must deal," including the legacy of human slavery and racial discrimination.

Even with these largely unnoticed qualifications, the Orlando speech was high on provocative rhetoric, which makes sense if you regard the world as a provocative place just now. My own notion is that without occasional reference to fundamental values, the great and scary conflicts of our time may come to seem mere perversities.

That is assuredly the case with the arms race, over which so much indignation is expended, even by professing secularists. If there were nothing more than prosaic national interests at stake --petty quarrels over borders and the like--the scale and seriousness of the rivalry with the Soviet Union would make little sense indeed.

It becomes intelligible only if one understands that two sharply different views of human nature animate it: the view of man as a creature of God, meriting the dignity of that image on one side; the view of man as a manipulable slave of the state, "history," or the "class struggle," on the other.

It was not mere whim that drove Lenin to say harsh things against religion ("a kind of spiritual gin . . . unutterable vileness"). The view that man is not the ultimate reality is a great impediment to just such demonic human will as he exercised.

For most purposes, these issues may safely be left to the pope and the bishops, who are not suspected of national self-interest. No state or system perfectly embodies the doctrines it professes, Judeo-Christian or Marxist- Leninist. But doctrines do differ, and the differences matter.

The president, as leader of the coalition of free nations, can hardly afford to be silent because his beliefs happen to scandalize tired secular sensibilities in his own camp. Why give unchallenged access to the world's attention to the Soviet Union's tireless crusade against the values that underlie the institutions of freedom?

In the end, the president's critics seem to propose a unilateral disarmament by silence. It may be as dangerous in the field of doctrine as of armaments.