What is distressing is that Mystery and Uncertainty do not represent good examples of the principles that Gawande demonstrates he understands in the first section, supporting his assertions with vivid anecdotes instead of reasoning from principles.

On my first reading, I interpreted "supporting his assertions with vivid anecdotes instead of reasoning from principles" as applying to the first section you were comparing the others to. After reading the full context, it seems you meant it to apply to the sections Mystery and Uncertainty, which makes more sense.

Suggested rewrite:

Unfortunately, in Mystery and Uncertainty, Gawande supports his assertions with vivid anecdotes, unlike the first section in which he used reasoning from principles.

Also, did Gawande back up his reasoning from principles with scientifically gathered data? This would make the point more powerful.