I enjoy the message of this article - one of support, and admiration.
That said, you're 100% correct about the way the article is written. The author notes at the end:
[Author’s note: While the Gay and Lesbian Alliance Against Defamation (GLAAD) recommends that the media use male pronouns when referring to Jenner, stating that “at this time, Bruce Jenner has not indicated that a new name or pronoun should be used,” I disagree. Since Jenner told the public that she has never fully thought of herself as male, I don’t believe that we should necessarily defer to using male pronouns just because that’s how Jenner has been referred to in the past.]
That sounds nice an all, but what it does is completely remove Jenner's agency in the matter. Jenner says "use male pronouns", then use male pronouns, or at the very most, use gender neutral pronouns. Using female pronouns without their permission or consent is just as bad as posting photos of them in a dress in the daily news, and is just as much of a breach of agency.
However, if Jenner said "Use female pronouns", then all future articles should use it for all aspects of their life, past, present, future. While this seems strange at first, you have to realize that this person has always been their chosen gender, even though they weren't necessarily able to show it. It also creates linguistic and editorial clarity (which, as evidenced in this article, can make it difficult to read when the pronouns aren't all sync'ed up). No switching from m to f pronouns necessary - just use them all the time.
Edit: as a side note, this is why 3rd person singular is SO USEFUL. Don't know which pronoun to use? "They" will do!