From article: "The challenge now is to document the claims of these witnesses about the secret ties between Saddam, al Qaeda, and Abu Wael."
MA: "On that sentence rests the journalistic integrity of the piece. I could wish it were within the first three paragraphs, where most readers are likely to find it, or even on page one, but at least it's there."

[You probably won't "get" how wrong this is, but I'll give it a shot.]
First: Why? Don't all the stupid readers flip to the back page and read how it ends?
Second: It was part of the conclusion, conclusions go at the end of the thingy.
Third: By putting at the end, it is saying despite all which said in the article, it is indicating that the author has not "got enough", and more work needs to be done. If instead the author had put near beginning the reader might get the false impression, that what follows is fullfilling what is needed.