On church councils and truth

While reading around the internet, I came upon a forum discussing the deuterocanonical books.

One interesting statement compared the doctrine of the trinity and it's 'official acceptance' by the church. The point was made that, even if the catholic canon was not accepted until after Martin Luther, usually the church only rules on things because they are being challenged.

However, it is not the ruling of the church which makes something true or not. We don't accept the idea of the trinity because the church accepted it. We accept it because it is true, and this evidently from reading the Bible.

So it is not any particular council which determines the truthfulness of something. A thing is true or it is not. Particulary when considering doctrine.

Does this apply to the canon?

Regardless of the councils decisions on the matter, what is the truth concerning the extra books?

The same article said that these extra books were excluded because they went against Protestant theology. The problem is that they also went against Biblical theology. There are some major doctrinal problems in the deuterocanonical texts. This leads one to imagine that the Church at the time could not reform their idea on these books because it needed them, based on previous tradition. Also, one must admit that the Church at this time did not have a great deal of integrity when one considers that she was selling salvation, via relics, etc.

How can one accept the decision of a Church who encourages pratcises completely in opposition with the teaching of Christ and his disciples? Obviously I'm speaking about the Church as it was at the time of the Reformation.