The main argument is based not just on a dubious manuscript, but on a dubious interpretation of that manuscript.
The Mar Saba Letter
In 1958, Morton Smith—a history professor at Columbia University—was looking through documents in the monastery of Mar Saba when he found (he claims) a letter written by second century theologian Clement of Alexandria to someone named Theodore. (Smith's translation of this letter can be found here. The original document has since been lost, although photographs survive.)
Secret Mark
In the Mar Saba letter, Clement claims that after the death of Peter in Rome, Mark traveled to Alexandria where he composed a secret, "more spiritual" version of his gospel, with additional teaching "for the use of those who were being perfected."
Clement quotes two passages from Secret Mark, both of which he claims were added to what is now the 10th chapter of Mark. The first is a rather lengthy passage that resembles the resurrection of Lazarus in the Gospel of John.
And they come into Bethany. And a certain woman whose brother had died was there. And, coming, she prostrated herself before Jesus and says to him, 'Son of David, have mercy on me.' But the disciples rebuked her. And Jesus, being angered, went off with her into the garden where the tomb was, and straightway a great cry was heard from the tomb. And going near Jesus rolled away the stone from the door of the tomb. And straightway, going in where the youth was, he stretched forth his hand and raised him, seizing his hand. But the youth, looking upon him, loved him and began to beseech him that he might be with him. And going out of the tomb they came into the house of the youth, for he was rich. And after six days Jesus told him what to do and in the evening the youth comes to him, wearing a linen cloth over his naked body. And he remained with him that night, for Jesus taught him the mystery of the kingdom of God. And thence, arising, he returned to the other side of the Jordan.
The second passage is short, and contrasts Jesus' teaching of this man with Jesus' actions toward the man's sister and other women who were present.
And the sister of the youth whom Jesus loved and his mother and Salome were there, and Jesus did not receive them.
The Carpocratians
Theodore had written to Clement, concerned about a gnostic sect known as the Carpocratians, who had obtained a copy of the secret gospel and were claiming that it promoted their libertine view of sexuality. Clement assures Theodore that nowhere does the secret gospel contain the phrase "naked man with naked man".
Analysis
The discovery of the Mar Saba letter has raised a number of questions.
- Is this an authentic letter from Clement of Alexandria, a forgery, or a hoax?
- If it is authentic, is "Secret Mark" an authentic expansion of Mark's gospel, or a forgery?
- If Secret Mark is authentic, does it promote sexual libertinism?
On the first question, scholars are divided even after more than 50 years of study. Handwriting analysis has led different scholars to opposite conclusions.
Many who consider it a modern fake have noted that the phrasing seems to have been deliberately chosen to sound ambiguous to the modern layperson.
Of those who believe the letter is authentic, most doubt the authenticity of Secret Mark, primarily because secrecy was a hallmark of gnostics and therefore was shunned by mainstream Christianity. A few scholars, however, believe the additions Clement quotes may have been authentic and possibly were based on an oral tradition of the Lazarus story. A small minority have suggested that Secret Mark was actually an earlier version of the gospel than the one which appears in the New Testament.
Of the scholars who accept the authenticity of both the Mar Saba letter and Secret Mark, most agree that the phrase "taught him the mystery of the kingdom of God" refers to the rite of baptism, based on the use of that phrase in other ancient Christian writings. However, one scholar, Scott Brown of the University of Toronto—the first person to do his PhD dissertation on Secret Mark—claims this refers literally to teaching.
Conclusion
The Mar Saba letter says nothing about Jesus' sexuality, and no scholar who has looked at it thinks it even implies that Jesus might have been gay. Some modern laypeople, however, have picked up on the unique phrasing of the letter to advance the idea that Jesus might have been gay.