Can a man who divorces after 'coming out of the closet' get custody of his children,in an Israeli court ?

There is no automatic bar under Israeli law  preventing  a homosexual father becoming a custodian of his minor children, just because of his sexual tendencies. If a custody case gets underway between him and his ex-wife, at the family court, then most probably a neutral court-appointed clinical psychologist will be appointed to make a report and recommendations on custody. The court will have to decide which parent has superior parenting skills, and whether it will be in the children's interest to be with the mother, or the father.

In general, courts tend to favour mothers, rather than fathers,  as custodians, especially where young children under the age of 6 are concerned, because of the built-in legislative bias towards them, though it is possible for a father to get custody, where this is in the minors' interests and welfare (e.g. where the mother is very career-oriented and has poor parental skills, or is a drug addict/prostitute etc, or has no or poor parental skills for some other reason). Where the father is a homosexual, he may have to invest a lot of time in overcoming prejudice, and persuading the professionals appointed and the court that his private life and sexual tendencies do not have a negative effect on his parenting skills, and that it is still in the children's interest and welfare for him to be the custodian.

Incidentally,there is also nothing theoretically, preventing a homosexual father from making an agreement whereby he gets custody, if the mother is in agreement. Any agreement about custody between parents - whether they agree it should go  to the father, or the mother, is is joint between them- must be authorised by the court.