I've reread the article a few times since reading your post, and while I might moderate the severity with which I first lashed at the author, I stand by my assessment. Here's my rationale:
1) The tone of the article is skewed in Harkonen's favor right from the outset, particularly in the way the author initially and repeatedly presumes the purity of Harkonen's motives ("saving lives"). In fact, we have no evidence of any motives other than the financial ("billion-dollar market," "$500 million opportunity," etc.).
2) Harkonen's methodology was flawed, full stop. While there might well have been something promising in the cohort he analyzed, a remainder cohort from one study does not take the place of a full set of clinical trials. Medical and statistical ethics would demand another study be conducted of the cohort Dr. Harkonen identified as more promising. Jumping the gun was unwarranted and possibly reckless. (As it turns out, a full study was later conducted, and indeed it proved the recklessness with which Harkonen leapt to his early conclusions).
3) Harkonen grossly misstated the results of the study in his press release, and, while it's hard to prove his intent, he is on record stating his financial upside in so doing. The author devotes all of a couple lines to this crucial point, then trots out a couple of irrelevant character-witness quotes to pave it over. (One quote essentially states 'If this is a crime, then a lot of scientists are in trouble!' Well, it is a crime. And if lots of other scientists are similarly cherrypicking their data and making misleading statements about it, then I'd say we have a serious problem on our hands.)
4) Your point about the closing statement in the article doesn't indicate absence of bias in favor of Harkonen. It adds some balance, yes. But it's buried at the bottom of the piece, where the typical reader either won't find it, or will glaze over it.
5) The opening paragraphs of the article, by contrast, paint a tragic portrait of an eminent and well-meaning doctor humiliated and punished for the crime of simply being overeager to help people (with the strong implication that his humiliation and punishment were unjust).
6) The author makes the repeated assertion that there is 'nothing factually inaccurate' about the content of Harkonen's press release. This is true by the letter, but not by the spirit. Harkonen cherrypicked the "facts" that he portrayed, accurately or otherwise, in that press release. And the later study bears out the potentially disastrous consequences of his having done so, negligently and recklessly.
I'll grant you that "fraud" seems a little extreme in this case, and that's where the controversy lies. But we can demonstrate mens rea, and at the very least, Harkonen committed an act of criminal negligence. That he stood to gain significantly from his misleading statements is strong circumstantial evidence in favor of fraud, though the article doesn't give us enough facts to make a definitive claim there. At the very least, we see no evidence that Harkonen was doing this to save lives -- a point the author strongly and repeatedly implies throughout the article.