One director for two projects would be nuts. Quality would suffer and that person would be burnt out as hell.
My personal guess is that both TLoU2 and the new IP idea they had got greenlighted and her proposal for another game got passed over.
Changes are more due to actor improvisation than rewrites.
i do not want to believe ign, but at the same time no matter how much i like naughty dog and its games, i do not want to believe in them 100% as well. no company is going to throw their current employee under the bus for a person they just fired.
just use logic. think of a company, even the one you work for. there are a lot of politics that go around, and what seems like on the outside is far different that what internal employees think since they have that unique perspective. there are a lot of employees at naughty dog, 200+ people. not to mention the business-side of things at playstation, all of which can be valid sources that could have dropped some hints to ign. if ign did not break that story, we probably wouldn't even know amy isn't with the company anymore.
so i give ign the benefit of the doubt. i would not call them outright liars because at least they had the info that amy was even let go.
so what i am saying is there is probably some truth to that article made by ign, but they failed to communicate the truth properly.
hopefully the game press actually do their job.