Kotaku contacted multiple former PopCap employees, including George Fan, and while the story may have some truth to it, it's certainly not the whole story.
George Fan wrote this on Twitter:
There is certainly room for connection there, as if George believes the story is correct. However the other developers that Kotaku talked to say that George was simply part of a mass of 50 layoffs from PopCap which happened in 2012 - although they also say that Edmund McMillen's story about Fan may be true in that he did not want to make "freemium" games, but the big difference was that he actively did not want to be involved in Plants Vs Zombies 2.
Another former PopCap developer Allen Murray replied to McMillen on Twitter with a few more details, confirming that yes, George Fan was against going Pay-To-Win, but he was never involved in PvZ2.
As with most things, the truth seems to be somewhere in the middle.
Super Meat Boy creator Edmund McMillen claims that EA, after purchasing PopCap Games in 2011, fired Plants Vs Zombies creator George Fan because he objected to turning the sequel into a Pay-To-Win mobile title. Details below.
McMillen told this story about George Fan, the designer of PvZ, on the Roundtable Live podcast. The story he tells goes like this, although Edmund admits he's not sure of all the details.
Plants Vs Zombies 2 came out on mobile in 2013 and is a free-to-play game aggressively covered in microtransactions.
This is only rumour so far, as we have only Edmund McMillen's word on it, despite him also saying George Fan is legally allowed to talk about it. There could very well be more to the story too. On the other hand, with what's going on with Star Wars Battlefront 2 right now we imagine a lot of people at DICE feel the same way about EA. He and George definitely retweet each other a lot, anyway.
Plants Vs Zombies was a phenomenon for PopCap when it released in 2009 on PC, before heading to every platform. It found its biggest success on mobile, leading to EA purchasing PopCap and turning the sequel into a Pay-To-Win game. It is possible to play the game and not rely on microtransactions, but things get very difficult if you don't.
George Fan and the original ex-PVZ team are currently working on Octogeddon, which is supposed to get a release date and proper trailer soon.