Surprising new intelligence that the Soviet Union has started actual deployment of a lethal new air-defense system raises agonizing new questions about President Carter's decision to scrap the B-1 bomber and use the cruise missile as a substitute.

This alarming news about the SA-10 was contained in a top-secret briefing given to Gen. David C. Jones, Air Force chief of staff, on Jan. 26. The newest Soviet ground-to-air missile travels at five times the speed of sound and can accelerate up to 100 times tht force of gravity.

The unexpected appearance of the SA-10 in actual operational deployment far ahead of schedule deepens the debate over strategic arms. Originally designed to defend against intercontinental ballistic missiles, the SA-10 is now viewed by military strategists as a great threat to the new doubts about Carter's reliance on the cruise to follow the present B-52 bomber.

The SA-10's threat to the cruise missile is both highly technical and in some dispute inside the Pentagon. Stripped to its essence, the threat centers on the SA-10's extraordinary power to accelerate in seconds up to five times the speed of sound. That could be fast enough to reach and destroy incoming cruise missiles flying below the speed of suond even though it is as such low altitude as to be visible to ground radar only briefly.

Secretary of Defense Harold Brown testified behind closed doors to Congress last September that the SA-10 might be nearing deployment. In fact, the first hard intelligence was then becoming available that deployment could come in a matter of weeks (probably near the Baltic coastline). Obviously, deployment of a few initial SA-10 launchers has not the slightest imdediately effect on the U.S. cruise missile, which is itself far from operational.

The problem is not today but the early 1980s. Defense officials freely admit that the present-day U.S. cruise missile could become dangerously vulnerable to Soviet air defenses by 1982 and beyond. That is because of Moscow's ability to pinpoint unlimited funds on specific military goals, such as defending agianst new offensive weapons.

But the Pentagon's Defense Sciemce Board concludes that the cruise missile of 1985 will be superior to the present version and that offensive technolog can always stay ahead of defensive technology. Thus, the board claims, the U.S. cruise of 1985 will defeat the expected Soviet anticruise defense system.

It is precisely such logic - based on assumptions that the Soviet operate in predictable fashion - that so frightens the president's defense critics. The astonishing speed-up in deployment of the SA-10 is major new ammunition for these critics.

Official defense doctrine placed the full operational capability of the SA-10 sometime in the early 1980s. But that projection antedated Carter's decision to dump the B-1 and make the cruise missile the principal "penetration" weapon for strategic purposes.

The American cruise has both terrified Moscow and galvanized Soviet defense planners into extraordinary accomplishments. That has demolished comfortable assumptions by U.S. defense planners of a free ride for the cruise until the mid-1980s, at which time new-model cruise missiles could carry radar-deflecting countermeasures as aprt of their playload and defeat the SA-10.

President U.S. underestimates of Soivet technological breakthroughs have plagued the West ever since World War II. As one generation of weapons succeeds another, this country makes the same incorrect conclusions time after time.

The new intelligence discovery that the SA-10 is in active deployment will have immediate impact on Capitol Hill. A powerful case now can be made that the cruise missile, good as it may be, must be allowed to bear the full burden of this nation's future needs for a "penetration" bomber.

Accordingly, the vote in the House (scheduled for next week) on keeping the vestige of the B-1 bomber program alive is almost certain to go against the president's desire to kill the program once and for all. Likewise, new research-and-development money for a lighter, longer-range substitute - the F-111H - will also find a more receptive congressional audience.

Civilian officials at the Pentagon still claim the cruise missile will always keep ahead of developing Soviet defenses against it. Doubters of that benign theory have new ammunition in the latest intelligence about the SA-10, and they intend to exploit it.