Feels bad, but at the same time it may be a positive thing.
The stories for the Uncharted series hasn't been all that strong, even though they had tremendous potential. Uncharted 3 in particular.
Uncharted 2 was the best in the series, back when Bruce and Neil worked on it. Meanwhile, The Last of Us basically took Naughty Dog to a completely other level of amazing presentation values.
I'm sure she wasn't necessarily 'forced out', but had an irreconcilable difference of opinion. Which is a shame, because Amy definitely deserves a massive amount of credit for the Uncharted series.
I just hope the project isn't in jeopardy like the recent Sony Santa Monica game....that would be terrible news.