ASTONISHINGLY, President Carter chose to take a public position on Canada's national unity and the Quebec separatists' challenge to it. So far, he's done no great harm. But he's set a highly dubious precedent for himself.

It's one thing to comment on civil liberties, and the lack of them, in the Soviet Union or other closed and oppresive societies. Americans need not apologize for championing, abroad, the same values they have struggled for so long to preserve at home, for these are matters of morality and fundamental philosophy. Separatism, on the other hand, is largelu a political issue in Canada; to to extent that this issue turns on a fundamental principle, it is the principle of "self determination," which happens to be another of those human rights that American hold dear. And Canada, we might add, also happens to be as open and responsive a democracy as any in the world.

That is one reason why this country's leaders ought to be wary about any statement that smacks of interference in internal Canadian affairs. Another reason is the peculiar nature of the U.S.-Canadian relationship, which sets a high probability that any official pronouncements from our side of the border can only injure our interests there. A lot of Canadians worry about American intentions. Our population is 10 times the size of theirs. In recent years there have been several best-selling political novels involving future military invasions by the United States; the idea seems ludicrous down here, but a good many people in Canada evidently take it seriously. Even aside from fiction, there is the economic fact that some 60 per cent of Canadian industry is owned by foreign firms, the great majority of which are American. Presidential statements that sound innocuous down here sometimes carry quite a different overtone up there.

It is true, of course, that Mr. Carter was careful to say that the future of Quebec is a matter for Canadians to settle. But his own "personal preference," he added, is that the country remain united. Now that's something that Jimmy Carter, private citizen - of even Jimmy Carter, presidential candidate - can say with impunity. But President Carter is no longer free to expresse his "personal" preferences about how other nations ought to manage their internal affairs without having whatever he may say - however "personally" - assume the full weight of official American policy. And he didn't say this casually; he said it twice, once in an interview just before Canada's Prime Minister Pierre Elliot Trudeau arrived on Monday and again at his Wednesday press conference just as Mr. Trudeau was leaving, Mr. Carter had a precise purpose. Since winning the Quebec provincial election last November, the separatists have recurrently hinted that an independent Quebec would enjoy a warm friendship with the United States. Those hints are in response, of course, to the manifold questions about the future of a country with no military defense and an urgent need for foreign investment to create jobs. Mr. Carter was carefully warning Quebec not to count on support here.

But Quebec's separatists, in any event, would have to reckon on a lack of sympathy and understanding on this side of the border. The protection of national unity is basic to American political attitudes. It is a principle that was case-hardened in the vast bloodshed of our own Civil War and has never been open to discussionn since then. The demands of French-speaking Canadians for a separate culture have no real analogy in this country and are generally met with total incomprehension. As for investment in Quebec, even the hypothetical discussion of separatism frightens the businessmen and the bondholders in New York.

There's another reason for this country's not involving itself in an internal Canadian dispute, and that is the inevitable tendency of partisams on one side or the other of the issue to misread anything of substance that may be said by an American President. ManyCanadians will now feel that Mr. Carter's statement in behalf of unity was very weak tea - so restrained, in fact, that it might almost encourage the separatists. Meanwhile, in Quebec, it's far from clear that the specter of American "intervention" may not help precisely the people whom Mr. Carter was presumably trying to undercut. Quebec's future is "a decision for Canadians to make," he said. That's exactly right. He would have been wiser to leave it at that.