THIS IS a convulsive moment in the Philippines, the troubled colony-turned-ally whose welfare is of such great sentimental as well as strategic value to the United States. A commission appointed by President Marcos has determined that his government's earlier explanation of the murder of his chief rival, Benigno Aquino Jr. -- blaming it on a lone gun hired by communists -- was a fake. The commission found a military plot that, four of five commission members say, was directed by no less a figure than the chief of the armed forces, a bosom pal of the president's. In short, the assassination of Mr. Aquino, as he stepped off the plane returning him from self-exile in the United States in August 1983, has now been laid at President Marcos' door.

It is not simply that Mr. Marcos faces an unprecedented test of the manipulative skills that have kept him in power for 19 years. If that were all, friends of the Philippines could breathe more easily, since no leader is indispensable. The country itself is in crisis. The Philippines is a nation beset, thanks in part to Mr. Marcos' leadership, by an array of cares that would challenge the most legitimate and deeply rooted democratic leadership. It doubles the burden to have to handle economic rot, immense corruption and an insurgency, among other difficulties, without a leadership with legitimacy and popular sanction.

The American attitude could be crucial. But here it is necessary and embarrassing to say that it is not clear what the American attitude is. As it happens, President Reagan was asked about the Philippines in the debate on Sunday. He should have stressed the need to have the Philippines hew to the democratic way. But he didn't. Instead, he posed the American alternative -- supporting President Marcos, even though "things . . . do not look good to us from the standpoint right now of democratic rights," or opening the gates to communist power.

That left the State Department struggling to limit the presidential damage. It called upon Mr. Marcos to apply the law even to his close associate, the chief of the armed forces. But the question remains whether Mr. Marcos will figure he has a friend in the White House and can in the end ignore the State Department's tougher word.

We realize it is hard for a politician in an election campaign to double back and make another, corrective pass at an issue he's mishandled the first time around. In this case, however, there is an overriding national interest in disabusing Mr. Marcos quickly of any notion that he has Mr. Reagan's okay to stonewall.