The U.S. Court of Appeals here yesterday ordered the reinstatement of an Air Force officer who was discharged after he said he would refuse to fire nuclear weapons on a civilian target.

In its apparently unprecedented 2-to-1 decision, the court said the proceedings that led to the dismissal of the lieutenant were improper and that he must be reinstated to active duty and paid $9,999.99 in back pay. The court also ordered the Air Force to reconsider its cancellation of his promotion to captain and to delete certain references to his position on nuclear weapons from his personnel record.

The ruling by U.S. Circuit Court Judges David L. Bazelon and J. Skelly Wright drew unusually harsh comment from fellow Circuit Judge Roger Robb, who said the ruling "violates the sound and established principle that it is not the business of the courts to run the military."

Robb said in a dissenting opinion that the courts had no right to challenge the policy that "a soldier whose obedience to legal orders is qualified or selective has no place in the military."

The ruling could be appealed either to the full nine members of the U.S. Court of Appeals here or to the Supreme Court.

The case involved Lt. John H. VanderMolen, who was first assigned in Taiwan in 1967 as an intelligence officer involved in analyzing materials concerning the People's Republic of China.

Three years later, he was transferred to a missile launch officer's course at Chanute Air Force Base in Illinois. In one of his early classes, an instructor asked VanderMolen and other students if they had any qualms about their work with nuclear missiles.

VanderMolen said it was at that time that he learned that the U.S. nuclear deterrent strategy may be in part premised upon the "extensive destruction of large population centers" and that the persons who launched the missiles might not know where they were aimed, the court said.

After counseling by his superiors did not shake his belief, VanderMolen was removed from the program and reassigned to another Air Force unit. He said in his lawsuit that was the only action he expected as a result of his announced stand on nuclear weapons.

However, as the appeals court Air Force career "began to slide pre-pointed out yesterday, VanderMolen's Air Force career "began to slide precipitously," he was recommended for discharge, and received an honorable discharge over his protests.

The court ruled specifically yesterday that the proceedings that led to VanderMolen's discharge were improper because he was not given the right to counsel, the right to a verbatim transcript, and right to notification of specific allegations, and other rights required by specific Air Force procedures. It did not rule on his claim that his constitutional rights were violated by the removal.

Mary Ballus, the attorney who represented VanderMolen before the appellate court, said the Air Force currently has a written policy that would permanently disqualify persons with beliefs similar to her client's from duty involving nuclear weapons.

She said that since his discharge, VanderMolen has attended law school and is currently an attorney in Alaska.

Robb said in his dissenting opinion yesterday that he felt the Air Force was "entitled to discharge an officer who might refuse to obey a legal order, and I find no prejudicial defect in the discharge proceedings."

He charged the majority judges with having a "zeal to find something wrong with the discharge proceedings, so that this officer may be returned to duty."