A new collection of John Cheever short stories will be published after all. Chicago Judge Roger Kiley ended a legal battle by saying Cheever's widow, Mary, 74, must honor her contract with Academy Chicago Publishers Ltd. but said Academy Chicago cannot publish all 68 of the stories without her permission. He said a smaller number - 10 to 15 stories - would "certainly satisfy her obligations." The book was to come out this fall, but Mrs. Cheever of Ossining, N.Y., notified the company in February that she considered the contract to publish the collection void. In June she said the Chicago publisher was presenting the stories "in a way that is repugnant to me and is injurious to my late husband's reputation."