Christianity in the second century did not have the rigid boundaries that we might think it did. I think it is more appropriate to understand it as "sectarian." This includes "mainstream" or "apostolic" Christianity. Christianity was only in its youth. It hadn't figured itself out yet. It was trying to determine its relationship with Judaism, its understanding of Jesus, its view of salvation, its use of rituals, its hierarchy, its position on women, its sacred scripture, its interpretation of scripture, and so forth. For every one of these issues, there were Christians with several answers. And many of these Christians formed their own communities. They talked to each other. They argued with each other. They agreed and they disagreed. Sometimes the discussion became heated, turned nasty, included name-calling, false accusations, and real hatred.
Now we have usually identified ourselves with the Christian position developed by the "church fathers," which itself is a problem since their positions were diverse. They disagreed with each other, and after their deaths, some were declared heretics. What do we do with Tertullian who was a Montanist, and who essentially created the tradition of Christianity that would come to dominate the West? Or what about Origen whose theology was later condemned, and yet whose theology formed the cradle for all later eastern Christian traditions? So even our concept of "mainstream" Christianity as some monolithic homogeneous entity is a misnomer.
Enter the "Gnostics" such as the Sethians who wrote the Gospel of Judas. Were they Christians? Well, it depends on who you would have asked. Irenaeaus would have said, "No." But they themselves would have said, "Yes." And they would have said that Irenaeaus wasn't. The Sethian Christians understood themselves to be the only Christians who really got it, who really understood Jesus' message. The mainstream Christians were ignorant, and not real Christians in their opinion.
So again, we come to apologetics, and how it affects the study of Christian Origins. Do we continue to understand the second century from Irenaeus' perspective? Do we continue to allow his "orthodoxy" to be ours? Or do we allow other voices to emerge and be heard, the voices of people who self-identified as Christians, but whose voices were marginalized, suppressed and silenced? For me, the choice isn't even a choice. The only right thing to do as a historian is try to fairly listen to all the voices, and use that to reconstruct what was really going on between the many different Christians in the second century.