Gospel of Judas and its implication for Christianity

The Judas Gospel has been reported as if it should be shocking to believe for Christians. Yet Chrisitans, and Catholics in particular, should be well aware that the early history of the Church consisted in large part of refuting and expelling heretics of one stripe or another and, in turn, developing doctrine more fully and precisely in response to these attacks. Most of Christology was developed in response to the Arian heresy (a belief that Jesus was lesser than G-d). Much of the free will doctrine was developed in response to the Pelagians (original sin for non-Catholics).

I think this story may be a bigger problem for Protestants than Catholics. Catholics believe that the Bible has authority and is what the Church says it is because the Church posesses teaching authority and is endowed with inerrancy (belief that the Bible is without error) when speaking authoritatively on matters of faith and morals. So when the Church says Tom has two natures in one person, or that there is a Trinity, or that the Gospel of Thomas is heretical while the Gospel of Mark is not, Catholics can (and must) believe it. Catholics need to believe in errancy because the fountain of their faith is Christ and they believe he left the Church as his voice on earth.

But what of Protestants and the Gospel of Judas. How can they believe the Counsel of Nicea and the other early counsels that defined doctrine (including the doctrine of which texts are inspired or not)? The Bible did not come down from heaven, ready-made, and in codified form. Numerous texts floated around the early Christian Church. They were only fully codified some 300 years later, where numerous gnostic texts in particular were expelled. It's true the Gnostics thought they were Christians, but the Church said they weren't after an ecumenical (general) council (meeting of bishops). I'll explain what I mean this way -- my girlfriend believes in the Bible because she believes in the Church, therefore she must believe that excommunication was meaningful as well (as a result the Judas revelation has no impact on her religion because the Gospel was expelled centuries ago).

The real question remains: what of Protestants who have no theological basis for believing as Catholics do? Who tells them what to do about the Judas Gospel (I am not saying Catholics are told, more to the point that they take a leap of faith that many do not)? In the end, it seems, they must decide for themselves.