I get what you are saying. But for Ripley in particular, the reason people don't mind the fact she's girlbossing in the end is because she was accompanied by a squad of tough as nails marines who kick a lot of ass throughout the movie (they even save her from two facehuggers at some point), so the viewer gets a lot of testosterone heroes as well. She has moments where she's vulnerable and suffers from PTSD, she's empowered by her motherhood instincts which are redirected from her pain of never meeting her grown daughter to the newly found Newt, she gets a little weapon training from Hicks, etc.
Ripley could have been an insufferable girlboss, but it's the EXECUTION which made the difference.
Also, back then the girlboss was the exception, not the rule, and men weren't NEARLY as annoyed by them as they are today.