You make alot of good points but the opposite can also be argued.
It can be argued but there's no evidence for it.
There is a conflict between Paul and Peter mentioned in Galatians. However, I don't see any evidence for a division between Mary Magdelene and Peter in the Gospels. If the Gospels were trying to diminish the role of Mary Magdelene, they wouldn't have emphasized her role in discovering the empty tomb or (in Matthew) seeing the risen Christ before the male disciples.
The earliest Gnostic texts were most likely written a century or more after the events in the Gospels, so linking the first apostles to them in any way is a stretch.
I was more looking at the Gospel of Mary to show her and Peter at odds than the gospels of the New Testament. The longer the Christian movement went on, the more tension and factions increased. The apostles/disciples in the case we're talking are mere personalities or characatures by this point. They represent factions of early Christian groups. The gospel of Judas demonstrates this by having the other disciples betray Jesus while Judas stands by and does what he is told to do. Even in the Gospel of John, Jesus tells Judas to "do what you are going to do."
They don't represent factions. The "Gospels" of Mary and Judas were written by fringe groups in the desert a century after Mary and Peter lived. There is no evidence of a Marian or Judan(?) community in the sense that there were Johannine or Petrine communities. These were groups who were writing things a hundred years after the fact with the sole purpose of distinguishing themselves from what had become the established church.
If anything the existence of these writings indicates that there was already an established orthodoxy by the early 2nd century (represented by men like Papias, Polycarp, Irenaeus, Ignatius, and Clement of Rome, etc). If there wasn't then these writings would serve no purpose considering their readers would certainly have seen them as pseudepigraphical.
Judas had no followers because he died shortly after the death of Christ, and Mary didn't have a separate community at odds with the established church because otherwise she wouldn't have received such favorable treatment in the Gospels. The conflict depicted in the "Gospel of Mary" between Mary and Peter only proves that Peter was seen as the leader of the Apostles among the established church. This is further proof of the lack of a lasting conflict between Peter and Paul's communities, because if Peter was still seen as the defacto head late in the 2nd century then why was Paul still so honored by the church fathers of the time?
If the Gnostic "Gospels" were written several decades after the death of Jesus there might be some credence to the various claims about them, but they weren't. Even if modern scholarship wasn't in unison on the fact that they were written much later, the form of pre-incipient Gnosticism attacked in the epistles of the canon is rudimentary and hardly unified, suggesting these heresies hadn't yet reached their systematization.
