I think the article is a bit disingenuous for two reasons.

Firstly, the examples he cites are mostly from Byzantium where eunuchs, sometimes known as "beardless men", held great importance in the civil administration and the clergy- and he doesn't mention this at all! Eunuchs such as Narses, a leading general under Justinian the Great could rise to positions of great honour within the Byzantine empire and effectively formed a third gender. It was a eunuch in the example he gives of the monk being locked away to avoid tempting other monks- if castrated before puberty they would not grow a beard or have other traditional male characteristics.

Secondly, there is a large amount of countervailing evidence against Christianity being tolerant of homosexuality in the Middle Ages. If we take two of the most famous figures at either end of the Medieval Period, Theodosius I, Christian and last united Roman Emperor (died 395) and Leonardo Da Vinci (died 1519), one made laws against homosexuality and the other was charged with homosexuality as a criminal offence when living in Christian Florence. For much of the Middle Ages homosexuality was considered an offence in Christian territories. This provided a useful contrast with the pagan religions i.e. the old Roman polytheism where homosexuals such as Emperor Hadrian could hold positions of power.