I know this is going to sound a bit . . . contradictory . . . but the difference in my mind is in the motivation behind writing something.
I expect something published by an organization to be "faith-promoting" and positive. For example, I don't expect Sam Walton's authorized biography to go into great detail about the views of those who hate Wal-Mart, blame it for the collapse of the mom and pop grocery store and view it as the great corporate Satan ("Voldemart"). I don't expect Al Gore to publish a nuanced and balanced piece on the cost-benefit analysis of implementing radical environmental standards. (Don't take that as a position on either side of that issue. It's not; it's just an example of an emotional issue today.) I expect the "party line" in both cases - efforts to present the white-washed, cleanest version possible.
Negative analysis ("criticism"), otoh, should be held to a higher standard, since such writings are much like legal charges. When someone attacks integrity or claims some kind of extreme or sinister motive, the burden of proof is on them - and it simply is not good legalism or journalism to ignore vast amounts of evidence when serious accusations are being made. (A prosecutor who uncovers evidence that would clear the defendant but ignores it is subject to sanction and official discipline for good reason.) Unlike the courtroom, in the publication of a book there is no defense attorney to counter the prosecution's charges in real time - so I believe there is an increased burden on the one making the charges to present both sides - at least to the extent that there is compelling reason to question or doubt the central assertion. If there is compelling reason to not reach the author's conclusion, I believe the author has the moral obligation to disclose it - or, at the very least, to mention it in passing as a concern.
The best example of this in Krakauer's book is the fact that there is no long, unbroken string of violence associated with the LDS Church in isolation and most LDS members. There was a lot of violence in the early days, prior to the exodus to the Utah Territory - but that certainly wasn't all the fault of the church members, and it wasn't even extreme within the time and location. (and it actually wasn't extreme when it comes to historical religious conflict) Frontier violence was common, religiously based or not. The Mountain Meadows Massacre was an anomaly - horrendous, but not the norm by any stretch of the imagination. The Lafferty brothers, Mark Hoffman and other individually violent members certainly are not the norm in the modern church. They are the exceptions that prove the rule, frankly, and yet Krakauer tried to use them as examples of the norm. To do that fairly, he should have disclosed openly that there were other examples outside Mormonism and religion at large that were just as egregious and violent (more so, actually) - and that a better proposition would be that religion doesn't eliminate violence entirely - that it can be used as a justification, but that it requires a perversion of the norm to do so. If that had been his thesis, I would have little problem with the book.
Again, I know it sounds like a bit of a double standard, and I really hate double standards, but there really is an important difference in intent and purpose when it comes to organizational publications and things written to attack them - and that difference establishes important variations in the criteria used to judge them.
I see through my glass, darkly - as I play my saxophone in harmony with the other instruments in God's orchestra. (h/t Elder Joseph Wirthlin)
Even if people view many things differently, the core Gospel principles (LOVE; belief in the unseen but hoped; self-reflective change; symbolic cleansing; striving to recognize the will of the divine; never giving up) are universal.
"For every complex problem there is an answer that is clear, simple, and wrong." H. L. Mencken