While I agree with the general thrust of your argument, especially that Dan Brown is not a great historian, if for 'Council of Nicaea' we substitute 'the Roman Church', then is there not some truth in what he says?

The Church, at whatever point it was, decided the New Testament canon. They therefore chose which texts to include and which to reject, therefore the story that they wished to promote.

The Gnostics were condemned, notably by Irenaeus, and their writings were presumably suppressed if not burnt, given that we have, as far as I know, no copies of them until Nag Hammadi.

Not mentioned by Brown, at least in your article, but didn't Nicaea decide what it meant to be a Christian, i.e. the creed? The council was therefore very significant, even if not accurately portrayed by Brown.

You can take this next comment less seriously if you wish, but do you really believe that the person next to Jesus in Da Vinci's painting is a man? This may be something of an anachronism, but I don't think the trans movement existed in C1 AD, certainly not the surgical procedure.