I've been involved in some discussions lately with people who don't think there was controversy in the early Christian church over what we are taught today is religious truth.
One of the arguments seemed to deny the possibility that the New Testament that we have today evolved from earlier works and was actively edited, cutting out books that strayed from official doctrine.
http://www.earlychristianwritings.com talks about the
Q document (the not-extant book of Jesus' sayings, which is claimed to form, along with Mark, a common basis for Matthew and Luke), and also has discussions of many other manuscripts (like the
Gospel of the Egyptians), many which might have been heretical at the time. Here's an argument
against the Q source, which brings up an interesting point or two:
No-one had ever heard of Q
No ancient author appears to have been aware of the existence of Q. One will search in vain for a single reference to it in ancient literature. For a while it was thought that 'the logia' to which Papias referred might be Q. Indeed, this was one of the planks on which the Q hypothesis rested in the nineteenth century. But no reputable scholar now believes this.
Anyway, I'm getting off topic. I've also encountered arguments that the
Council of Nicea was basically affirming in the
Nicene Creed something Christians believed anyway. However, there are several examples of variant strains of Christianity that defy this logic. For example, in the middle second century, a form of Christianity sprang up known as
Marcionism. Marcionism saw the Bible as being from two distinct gods - the wrathful, angry god of the old testament, and the loving and merciful god of the new testament. Marcion was excommunicated from the Church of Rome around 144 AD, and his religion is described as the
Roman Catholic Church's greatest enemy.
Another example, of course, is the group known as the
Gnostic Christians. This group was in decline by the time of the Council of Nicea, but is still in existence in various forms today.
While neither of these groups were big at the time of the Nicene Council, there was a
group led by Arius which disputed the unity of God the Father and Jesus - in effect the widely held doctrine of the Trinity of today's Christian Church. The vote was not close, but any chance this view had of catching on was seriously undermined, even if the controversy lasted another hundred years.
I haven't found any sources that indicate the early Church was involved in hunting down these groups and burning their literature, as common wisdom seems to suggest, but it's hardly deniable that if your doctrine is denounced by the legal, dominant religion, it doesn't have much chance. So I don't find it unbelievable that the early Church might have suppressed a relationship between Mary Magdalene and Jesus.