There was some early writings that appeared to be "anti-gay", stating that homosexuality was covertly hostile. But one must look at that in the context of the times. In the 1940s - 1950s most people in western countries did consider homosexuality to be a mental or even physical illness.
I do not have any knowledge or evidence of anti-homosexual actions taken by the church at any point, other than the few writings on the subject. It was pretty much left alone for many years.
Then in 1967 Hubbard issued a policy which reads, in part, "It has never been any part of my plans to regulate or to attempt to regulate the private lives of individuals. Whenever this has occurred, it has not resulted in any improved condition... Therefore all former rules, regulations and polices relating to the sexual activities of Scientologists are cancelled."
Hubbard later released a book about ethical behavior that was silent on the subject of homosexuality, and offered a gender-neutral ethical guidelines about being faithful to one's partner and avoiding promiscuity.
The Church of Scientology is a leading proponent for human rights for all people of earth as can be seen by their campaigns with Youth for Human Rights and the Citizens Commission on Human Rights.
In October 2009 a spokesperson of the Church of Scientology International put it this way:
"The church supports civil rights for everybody, regardless of sexual orientation, race, color or creed. We are a minority, too; we understand what it’s like to be persecuted, so to the extent that anything prohibits or inhibits on civil rights, we don’t agree with it.” (MSNBC, 28 October 2009 / PDF)