I have the suspicion that men today believe in God more than at any other time in human history. Men know the gospel, the teaching of the Church, and God's creation better than at any other time. They have a profound consciousness of His existence. Their atheism is not a real disbelief. It is rather an aversion toward somebody we know very well but whom we hate with all our heart, exactly as the demons do.
We hate God, that is why we ignore Him, overlooking Him as if we did not see Him, and pretending to be atheists. In reality we consider Him our enemy par excellence. Our negation is our vengeance, our atheism is our revenge. Kalamiros: River of Fire
A lot of the atheism I've run into is of the above sort…that rooted in an aversion to "Someone" who is known but loathed. Given your description of your situation with your parents and upbringing I would not be surprised in your own views on God's being began in a similar context.
With respect to the question of homosexuality, Orthodoxy…at least as I've known it, while firm, is also nuanced in some interesting ways. One of the central concepts…experience in Orthodox theology is that of communion. We don't believe anything that exists, including God, exists absent communion. Love does not exist for its own ends or in the absence of the other. Thus God, being love, exists in the primordial communion of Holy Trinity. We regard communion as the very foundation of being. We are meant to live in communion with each other and with God. Our understanding of communion is pretty literal, we are meant to be one…inside each other, life flowing into life, yet without the loss of personhood, rather indeed having our personhood expressed and fulfilled in that communion. This life of communion with each other and with God we call the Church.
Given then that we are creatures created for communion, the desire to know and be known by another in love is part of the very fabric of our being. Unfortunately for us, we are also fallen beings, and our God given desires are often twisted away from their appropriate means of fulfillment. For example, we all need to eat in order to live, yet how many of us have eaten far more than we need, even to the point of severely compromising our health. Gluttony is a normal desire, a normal appetite gone awry. We call these misplaced, disordered desires "passions", and there are a range of them from anger to laziness to gluttony, to various disorderings of our sexual desires. Some of these things are learned behaviors, some are constitutional, some a bit of both, but that does not make them good and acceptable for all that. The man given to overeating must struggle against it regardless how "natural" it is for him to eat too much, no matter how good he feels when he indulges his appetite. In the end, unless he learns restraint, he will by his passion destroy his body and undermine any relationship with others that depends upon his having a healthy weight.
Bearing this in mind lets look at the issue of same sex attraction both in what is right and what is disordered about it as a passion. It is right in that it desires a deep and abiding union with another man. It is disordered in that it seeks to fulfill that that desire sexually in the body. Our bodies were not created for same sex fulfillment. They can be used in varying degrees in that way, and it can be pleasurable, but same sex bodily unions undercut, diminish, and work against the deeper communion we were created for…the communion that is the fruit of long intimacy, prayer, and joint ascetic labor. Consider, the deeper desire when seeking or communicating with a long term partner. Get past the biochemical sensations of arousal and copulation. What is your mutual nakedness if not an expression of the need to be completely known by another and to know them in turn, and to be safe in that mutual sharing of ones' unedited selves…to be lost, found, and accepted in the eyes of the other. There is a joy to be sure in the experience of that…but it is tainted and diminished by sex. The other's body becomes a tool for making us feel good for a few seconds…for a fleeting ecstasy of the body…an ecstasy than cannot fulfill itself in the creation of new life.
True communions lead to life. Bodily unions between those of the same sex cannot. But the unions of minds and hearts can lead to new life and to depths of intimacy far beyond any physical expression. If you read patristic literature, from time to time you will come across descriptions of these vast heart to heart intimacies that are known between two spiritual friends or between a spiritual father/mother and his spiritual child. Insofar that these types of communion in their fullness belong to man as he nears his healing they therefore consequently harder to attain than a variety of physical unions both legitimate or disordered.
One such friendship mentioned in Scripture is that of David and Jonathan, of who David says, his love is better than the love of women. Some would like to make this to be a sexualized relationship, but it was not…the fathers and saints who have known this sort of relationship themselves tell us plainly or show us through their lives. It exists.
Orthodoxy recognizes that there are a variety of saving relationships we know in our lives…relationships that tend to heal us and draw us nearer to God, making us more like Him. We know that of priesthood, of marriage, and of monasticism, and we also have rite called brother making, adelphopoeisis. It is the sacramentalization of a deep and presumably spiritual friendship…a saving friendship. It is ancient and has been both celebrated and suppressed throughout the Church's history. That is because, as might well be imagined, by it's nature it is open to insincerity and abuse. Some have tried to use it as a kind "gay" marriage. At other times in other cultures and situations it was used as a mask for subversive political activities…some not so peaceful. But still at heart, it recognizes the desire, and the need for intimate friendships in our lives, and unites that desire to the communion of the life of the Church…and that consciousness remains in Orthodoxy to this day.
It still recognizes and sacramentalizes every saving relationship open to us, but it does not stint to warn us that if we would be healed in our passions that will take careful labor, prayer, and the development of a simple and innocent heart. And it does not excuse a passion as desirable or call it healthy just because it is fashionable to do so. In Orthodoxy you will find that same sex intimacy is honored, blessed even…but only in its proper sphere of heart and mind. Deep, fervent, joyful, abiding love is blessed, but the union of bodies between man and man or woman and woman is not.