A courtroom battle which fused a fight over child custody inextricably with a debate on homosexuality ended here today when a judge decided against awarding two children to their lesbian mother.

After eight days of often inflammatory testimony, District Court Judge Roger Cisneros awarded custody of Audrey Lynn Stover 8, and Jesse Edwin Stover, 6, to their father, Harold, 41, rather than to Kathryn Stover, their mother.

Cisneros said that the mother's lesbianism wasn't considered in making the decision. He said he relied instead on expert testimony from psychologists, which tended to favor the father, in directing Mrs. Stover, 36, to surrender the children who had been living with her and lover. Ann Adams,34.

Despite the efforts of lawyers and witnesses to sidestep homosexuality as the central issue in the fight, Mrs. Stover's relationship with Adams was discussed in some detail by nearly every witnesses during the court proceedings, believed to be among the first custody cases in Colorado in which the sexual orientation of a parent has been aired in open court.

"I realize people keep trying to put the sex issue back into this as a significant issue, but there are other factors that certainly come first" in deciding custody, said Jean LaCrosse, a psychologist at Denver's Children's Hospital who was part of a three-person evaluation team who advised the court that they believed the children would be better off with their father.

But other psychologists had testified that Mrs. Stover was capable of giving the children more of what they needed than the father, and that her homosexuality wouldn't be an impediment to the emotional health of the children.

Cisoneros, however, apparently found more compelling the testimony of psychologists who indicated that Mrs. Stover was going through a period of self-assessment, which would likely take away from the attention and affection she could give to her children. One psychologist said from the witness stand that Mrs. Stover seemed "self-centered" and showed a prefernce for tasks that did not involve being around young people.

The husband, on the other hand, was characterized by friends of the family as dedicated to the children and inclined to devote whatever time is required to their development.

The bitter courtroom proceeding ended in a manner that paralleled a recent ABC-TV program, "A Question of Love," in which a lesbian woman lost custody of her children.

The Stovers were married in August 1965 and separated last March. At that time the two children went to live with their mother.

Unsuccessful attempts to exclude the press were made by lawyers for both sides early in the proceedings. However, once Cisneros ruled that the media were welcome, a flood of local reporters converged on the normally quiet courtroom.