It's not just about mislabeling, or false accusations. There is a certain element of hypocrisy, too.
A demonstration of this is in the article:
"In May, the company banned harassment of individuals from the site. Last month, we took down sections of the site that drew repeat harassers. Then, after making these policy changes to prevent and ban harassment, I, along with several colleagues, was targeted with harassing messages, attempts to post my private information online and death threats. These were attempts to demean, shame and scare us into silence."
On one hand, these people affiliated with reddit did not appreciate these alleged "attempts to demean, shame and scare us into silence" when they were the recipients.
Yet these same people were perfectly willing, and perhaps even proud, to silence other reddit users, whether at an individual level or by eliminating entire subreddits.
In fact, the article in this case could very well be seen as an attempt to "demean, shame and scare" the alleged "trolls" into silence. It engages in the sort of behavior that it is deeming as unacceptable!