The honest Bible writers reported on skeptics. We have skeptics now and then. But a gospel or epistle recounting a resurrection and a dozen miracles of Jesus, with a half-verse about contemporary skeptics, is not a counter-document.
By counter-document, I don't mean "Some who saw His miracles or heard His teaching disbelieved when we reported we'd seen the risen Christ," a natural response for anyone, really, but a true counter-document, "I lived in Jerusalem at the time and Jesus did NOT reprove the Pharisees, heal a blind man, preach to thousands, etc., etc., etc., etc. as reported/preached".
In Pagels book The Gnostic Gospels there are many accounts of Gnostic christians calling what the bishops were teaching (similar to current orthadox) as heretical and false.
"He denounces as especially "full of blasphemy" a famous gospel called the
Gospel of Truth. Is Irenaeus referring to the same
Gospel of Truth discovered at Nag Hammadi' Quispel and his collaborators, who first published the
Gospel of Truth, argued that he is; one of their critics maintains that the opening line (which begins "The gospel of truth") is not a title. But Irenaeus does use the same source as at least one of the texts discovered at Nag Hammadi--the
Apocryphon (Secret Book)
of John--as ammunition for his own attack on such "heresy." Fifty years later Hippolytus, a teacher in Rome, wrote another massive
Refutation of All Heresies to "expose and refute the wicked blasphemy of the heretics."
This campaign against heresy involved an involuntary admission of its persuasive power; yet the bishops prevailed."
Excerpt from: The Gnostic Gospels by Elaine Pagels -- The Nag Hammadi Library
There was eventually a blackout period where all counter evidence was destroyed. Pagelas touches on this from the Gnostic perspective in an interview:
I would say that in the early Christian movement, many different groups claimed to have the best possible understanding of Jesus. And one of those groups which was widely consolidated and widely spread prevailed over the others. You can give it that kind of very negative read, and some of us may agree about that. But they were, from their point of view, trying to salvage the church as they saw it.
Q: Why was the church afraid of the Gnostic Gospels?
A: The people who disliked these other Gospels included leaders such as Bishop Athanasius, who was very much concerned about establishing his authority over all the monks in Egypt.
Q: And who ordered them burned?
A: Right. These books were treasured in one of the oldest monasteries in Egypt by monks who saw them as guides to spiritual development. There are monks today who see them that way, as well. But the bishop, who wanted authority consolidated in himself, told them, “Get rid of all those books. You don’t need all those books. All you need are the ones that I will mention now.” He mentions a list, which is our first list of the 27 books of the New Testament. He told them, “Get rid of your library, and just keep these.”
Q: Do you think that belief in Jesus as God has been overemphasized in Christianity?
A: I think it has. Christianity as we know it is almost defined as belief in Jesus as God. What we lose when we see it that way [are] many other perspectives. The Gospel of Mark doesn’t picture Jesus as God. The Gospel of Matthew doesn’t picture Jesus as God. Matthew pictures Jesus as a rabbi, as a new Moses who teaches the divine Torah — “You shall love the Lord your God with all your heart, and your neighbor as yourself.” In the Gospel of Matthew, Jesus says to people, “Do not call me good. There’s only one who is good, and that is God.” The Gospel of Matthew does not suggest that Jesus is in any way God. It is a much more traditionally Jewish book which speaks about love of God and love of the neighbor as the essential devotion of any person.
October 10, 2003 ~ Elaine Pagels Extended Interview | October 10, 2003 | Religion & Ethics NewsWeekly | PBS
But Richard Carrier often mentions the "blackout" period were we have no information from detractors because this material was not allowed. The only reason the Nag Hamanndi fragments were found was because they were deeply hidden in a cave.
Once Rome took over counter examples were punished by death.