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I can't say for certain that Manjoo is correct, but he appears to be using the tools of reason and logic with detailed references to make his points. I do know that if Manjoo had found compelling evidence that the election was rigged that he would be sitting on a major story, which would in all likelihood make his career.
It takes a certain degree of paranoia to assume that Salon is in the business of hiring right-wing shills to deceive its readers. It is however perfectly credible that Rolling Stone would publish a known controversialist with little credibility to hype a largely discredited conspiracy theory in the hope of increased sales.
I would suggest that one way to tell good journalism from bad is that good journalism occasionally presents the readers with stories containing truths that they would really rather not hear. The sort of stories that cause numerous readers to write in demanding to cancel their subscription. This would suggest to me that the publication is trying to prioritize truth over pandering to their readership.