According to the ArtsBeat piece, the ending of "Finding Dory" involves a marine park. That plot point remains -- but now, according to a Pixar employees, the sea creatures have the freedom to leave.
"Finding Dory" won't be released until 2015, so the script change doesn't affect production.
"Blackfish" distributor Magnolia Films released this comment in response to the change: “We think it speaks to the integrity of Pixar that they’d be moved to revise the story of 'Finding Dory' because of the revelations in 'Blackfish.' We’re ecstatic that Gabriela’s powerful doc is making this kind of cultural impact.”