I personally believe the original report that she was lowkey bullied out of Naughty Dog because Neil Druckmann felt like he was riding on a higher horse after the success of TLOU, and in many ways he also had a better grasp of what people expected of Uncharted 4. The problem is, he's such an inferior writer just when it comes to prose, characterization and dialogue, and Uncharted 4 suffered without Amy to handle its final drafts. Tonally it also faltered. While I would say Uncharted 3 also had tonal inconsistencies it was more the contrivances that bugged me than the occasionally awkward usage of different narrative genres.
When musicians collaborate, there's many stories of clashing egos, and you'd be gullible if you think it never happens in game companies.
As for Amy and EA, well... they have patrick soderlund and all these "money and fast cars" kind of executes around them. In this business, as most businesses, the money is the bottom line for various reasons but at EA it's clearly the reason people in higher up positions come to work there, whereas I believe companies like Sony or Nintendo have more ethical or artistic concern at the top alongside their business-minded employees. Ultimately, as Amy said that's why her work didn't make it out. "It didn't fit with EA's business plan". It's not the branding of the game that wasn't good enough, it wasn' that they didn't believe in the pitch, it's just that EA decided that the business model did not fit with the project.