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I haven't read this article in particular but I am familar with Elain ePagels. She writes very well and has a way of writing that is very good to non-academics. The only complaint I have about her is that she's of what is a bit of an old school of thought concerning the Gnostics, that they were some kind of distinct movement. Prior to 325 CE, there was no universal orthodoxy. Christianity was defined by whatever community you were in. The Christianity in Jerusalem was different from the Christianity in Corinth and different from the Christianity in Rome. In general you had three broad categories: Jewish Christians, Gentile Christians, and Torah-observing Gentile Christians. Gnostic was a slur for any group of Christian Ireneaus didn't like. The only group that probably called themselves Gnostic were the Sethians. It should also be noted that prior to Ireneaus, gnostic was an archaic term for the word saint, since the saints were "known by God and knew of God". Ireneaus uses it in a mocking fashion like, "know it all". I don't see conflict with the Gospel of Thomas or John so I doubt personally that John was a rebuttle to Gospel of Thomas. John is basically a combination of theology overview, creation story, and gospel all wrapped into one. There are many double, triple, and quadruple meanings in the passages of John that get glossed over since English is kinda flawed in this department. The opening passage of John makes it clear that it is a "Gnostic" texts.

Much of the "Gnostic" stuff did get absorbed into what became Orthodox/Catholic Christianity. Sainthood is salvation by gnosis. The Eucharist was a gnostic ritual. The Virgin Mary is a literary foil to Sophia. Most of the letters of Paul were used by gnostics. The Trinity has roots in Gnostic, specifically Valentinian theology. Also for a while, these texts in the Nag Hammadi Library were used in Orthodox/Catholic monastaries as supplimental documents, up until like 4th/5th century when they were ordered to be destroyed. Thankfully someone saw value in them and tried to preserve them the best they could at the time.

For anyone that's interested in this topic, Elaine Pagels is a great starting point, but you might want to move on to other scholars such as David Brakke, Karen King, or Michael Williams.