Any reading of texts either in early, middle or late history shows that heretical sects have always been present (at least they are heretical from the standpoint of those that won history). You don't need any newly discovered texts to garner that piece of information - it's in the New Testament that there were all sorts of disagreements going on in the early church - Paul being quite upset in a number of places, in an attempt to define orthodoxy. It's more of a Protestant theory that the Church was somehow without dissent at some point in early church history and it was the Catholic Church that led everyone astray from the ideal (sometime around the time of Constantine). The Catholic Church knows full well that the Biblical Canon is not something that happened out of thin air. Texts that are not included in the Canon are sometimes considered to be authoratative in the same sense as Jews consider the Talmud to be relevant. On the other hand, the Catholic Church is also aware that what's in the Canon has not always been 100% agreed upon. For the Old Testament, there are 70 books in the Catholic version, 74 in the Orthodox version, whereas the Protestant version is 60 books (which agrees with the Jewish Version that was canonized in 190AD).

The controversies that have faced the church have defintely changed over time. In the very earliest controversy, there's the question of James vs. Paul (Jewish vs. Greek Christians). Then as the Church spread through the Greek world, there's the Gnostic influence. The Gnostics rejected the Old Testament - i.e. they rejected all things Jewish - and they were more into the mysticism and hidden knowledge. The Gospel of John shows quite a distinct gnostic flavor. Later, there's the question of Roman influence as the Christians went from being a persecuted group to being the powers that be. The Nicene creed was more influenced by gnostic thought than was that of the accursed Arius.

Anyhow, the Catholic Church does not view the canon as being something that was somehow delivered in full at some point in history. There was a fight for inclusion of some texts that didn't make the final cut. And there was some descent on other texts that were included - Revelations being a minor point of contention. What the Catholic Church has always held is that it is within the power of the Church to define what the "official" teachings of the Church are to be. It's that authority that came to be the major point of contention during the Reformation.

All these historical controversies are fairly meaningless in modern contexts. There's still the occasional spate, but the problems that face the Catholic Church in particular, or Christianity in general, have little to do with this ancient history. The Gospels of Thomas or Judas are just fragments from long ago that were not passed down as church teachings. They may shed some light on the history, but they will ultimately just lead to people interpreting these things in all sorts of different ways - Solo Scriptura was a much more radical departure than anything that has happened subsequently or is likely to happen in the future. The Church was no more perfect in the hours that occurred immediately after the cruxificion than it was some 2000 years later. Or if you wanted to put a negative spin on it - the Catholic Church believes itself as perfect today as it was 2000 years ago - and there are as many heretics now as there ever was.

Anyhow, I think you overestimate the findings. The level of discomfort in the Catholic Church is minor if at all. But, then they don't particularly care to give anyone cause to read the texts from what they say. If they came out and said that these texts are forbidden to be considered as part of church teachings, the likelihood is that it would lead to a frenzy of people buying a copy - and that's the more troubling matter from the Catholic Church's standpoint - it's power is definitely not what it once was - either moral or political.

In terms of a book of Judas, a book that was much less gnostic in nature would be more believable. That is, Judas is a caricature of sorts of the Pharisees. A true book on Judas would be much less influenced by greek thought. If it turns out to be gnostic in nature, it might be interesting to analyze history, but it'd be a total fabrication from the standpoint that it arose from the Jewish Christain sect. It was quite common at the time to use a known name as the authorship for texts. For example, it's hard to know exactly who exactly Matthew, Mark, Luke and John were that wrote the four gospels, whether they are who they claim to be, whether it was written down later by one of their followers, whether it was a collection of writings that were assumed to be from that name, or whether it was just a borrowed pseudo-name. About the only thing we know for sure is that Paul's personality is so overbearing that we are pretty sure that he was the author of all the texts assigned to him.

...it might also be noteworthy to suggest that very few religious texts stand on a firm authorship ground (unless we are discussing L Ron Hubbard). Most of the Torah was written down well past the time of Moses. Genesis in particular has two creation stories, and also some weird subtexts that are seemingly along the lines of greek type mythology.

The Quran might seem less susceptible to redaction, but its authorship is not particularly well established. With Mohamed being supposedly illiterate, it's unlikely he wrote the text. More likely that his followers wrote it down sometime during and/or after his death. Though there seems to be some thought that the authorship was purely divine - which means that its basically unknowable - we know its Gods word because God wrote it type of reasoning.

You'd probably find similar problems with the Hindu and the Buddhist texts as well - supposing one were inclined to a methodical objective analysis. But such literary analysis problems aren't likely to phase the believers, since leaving the question open usually lends a certain quality of mysticism - something that never seems to hurt in that line of business.

If you are a believer in one of the historical based religions (Christianity, Judaica, Islam, etc...), then I'd think that you'd have to admit that God mostly acts through man. And anytime you enter man into the equation, you pretty well have skewed history very much on the side of imperfection.