Retracting a report that they didn't think they could legally defend in court is a long way from justifying comparisons to Nazis.
Personally I would have rathered that they removed the report and released the information from the perspective of the US chapter with mildly revamped wording, but I get the course of action.
I'm not convinced it would be a pr coup or net financial win for them to publicly be unable to prove that "gender critical" organizations are defacto anti-rights in general, or that Rowling's sexual violence charity that was mentioned in specific was.
When the argument is that they over generalized and named organizations as guilty by association without justification, they wouldn't be arguing trans rights or equality but specific public policy stances.
Appearing to argue that a rape support center is in violation of human rights by catering to cis women isn't going to be the pr coup.
It doesn't matter that they're clearly anti trans and founded because the alternative didn't exclude trans women and had a trans director: amnesty would need to show they were an an anti rights organization.
I'm not saying that I like that they took down the report or apologized. Nor am I saying that any of the groups are accepting or good.
I'm just saying that Rowling and the stupid uk libel laws are better targets for ire.