Reading the Bible as Literature?

My son attends a small, conservative Christian college, and he's taking a summer class called Encountering the Bible.

Almost daily, he expresses his displeasure with how the textbook and the instructor are interpreting God's Word.  

He's complained about teachings such as:
- Heaven and earth existed before God began His work of creation (that God didn't create them).
- Daniel was written around 150BC (not 530BC) because Daniel couldn't possibly have made accurate, historic predictions.
- Luke didn't believe in the atonement.

Also, some students are saying that the course is causing them to doubt the validity of the Bible.

The class appears to be using the historical-critical method of evaluating and analyzing literature.  I call this approach the "text can't mean or be what it claims to be, so let's analyze it" method.   

I'm aware of some of the thoughts related to higher criticism.  However I find these ideas to be subordinate to how the Bible testifies about itself.

It comes down to, "Can we use our human theories and techniques, our own reasoning, to analyze God's Word?"  

For my thoughts are not your thoughts, neither are your ways my ways, declares the LORD.  For as the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts.  Isaiah 55:8–9

The Lutheran Confessions (The Formula of Concord) puts it this way:

We cannot harmonize God's revelation with our reason, which we have not been commanded to do anyway.

God's Word isn't like any other literature.  In reading it, we have to consider God's character and His intent.

1.  God wants to give us and show us His love and mercy; that's His nature.

But you, O Lord, are a God merciful and gracious, slow to anger and abounding in steadfast love and faithfulness.  Psalm 86:15

2.  The Bible is all about Jesus; it must be read through that context.

Then he [Jesus] said to them, “These are my words that I spoke to you while I was still with you, that everything written about me in the Law of Moses and the Prophets and the Psalms must be fulfilled.” Then he opened their minds to understand the Scriptures.  Luke 24:44–45

God's Word is powerful.  I struggle with it because it always convicts.

For the word of God is living and active, sharper than any two-edged sword, piercing to the division of soul and of spirit, of joints and of marrow, and discerning the thoughts and intentions of the heart. Hebrews 4:12

But His Word also comforts. 

The LORD is near to the brokenhearted and saves the crushed in spirit.  Psalm 34:18

And no matter what we may think about using our own theories, logic, and reason, we don't have it all figured out.  

Every man is stupid and without knowledge.                Jeremiah 51:17a

But thanks be to God, who gives us the victory through our Lord Jesus Christ.  1 Corinthians 15:57