It should have been an instant winner. Sens. David Boren and Ted Stevens were offering their colleagues a chance to save money and no doubt lives at the same time. Their proposal was to stop subsidizing cigarette sales in military commissaries and post exchanges. Cigarettes now sell for about a third off civilian prices in commissaries, and a fifth off in exchanges. Surveys show that 52 percent of military personnel smoke cigarettes, as against 32 percent of the general population. The figure is also 52 percent for military personnel under 20 years old, as against 21 percent for high school seniors. Federal health authorities no longer quibble on the subject; "the surgeon general has determined that cigarette smoking is dangerous to your health," it says on the packages and in the ads.

Yet the Boren-Stevens proposal, a tiny patch of fine print in the $281.2 billion fiscal 1986 defense appropriations bill, failed. Part of the opposition came, predictably, from the tobacco industry, in the person of Rep. W. G. (Bill) Hefner, Democrat from North Carolina and an appropriations conferee. Part also came from the Pentagon, and organizations representing current and retired servicemen. Their chief concern was the commissary privilege. The commissaries are now required by law to sell goods so close to cost that they lose money. A cherished fringe benefit, they cost the Treasury about $600 million a year. Because cigarettes are responsible for over 10 percent of commissary sales, Sens. Boren and Stevens said that their proposal would cut about $77 million from this sum.

The affected groups were worried as much about the precedent as about the money. Let Congress raise the price of one product sold in commissaries and it might raise others. Defense Secretary Caspar Weinberger sent a letter of protest to Senate Appropriations Committee Chairman Mark Hatfield. "This provision would establish the precedent of decreasing savings to the service member to offset the appropriations for commissaries," he complained. "It is this commissary appropriation which is directly responsible for making the commissary an efficient means of compensating our military members and their families."

Instead of requiring the price increases, the conferees on the bill called for a study, to be completed by March 1. Fortunately, the study is to be done by the assistant defense secretary for health affairs, Dr. William E. Mayer -- and he has apparently already made up his mind on the subject. Dr. Mayer had already prepared, quite by chance, a recommendation that Mr. Weinberger ban cigarette sales in commissaries and let post exchanges sell them only if they raise their prices.

In similar circumstances in 1982, Mr. Weinberger raised the price of liquor at military outlets. What was wise in the one case is wise in the other. The secretary should do as the doctor suggests -- and shouldn't wait for Congress to tell him to.