I can't say I'm convinced. Normally, I kind of like Mother Jones, but their thesis that it was murdered is kind of built on an anecdote that I think they're blowing out of proportion.
There was definitely an issue with brand strength and identification with that brand, which meant that Coke's marketing for New Coke ended up in competition with their old marketing successes. They somehow had to push this new formulation while still tying it to Coke's timelessness, nostalgia, and the mystique of its 'secret formula'. They'd even sold Coke syrup as a home remedy for nausea for decades before trying to switch to New Coke. So, yeah, they faced a backlash that may have started as a smaller, hard core, but it was the more persuasive sentiment in the end.
Lesson to take away: be careful with any identification with the brand you try to generate with your marketing - it may prove stronger than your ability to change it.