Did either of you read the article? The control group picked "their least important values and wrote about why these might matter to other people." The article says nothing about how either men or women perform without a values exercise.
I don't think that exercise, in itself, would make anyone perform worse at physics. While writing about why your values are important to you could very plausibly increase your confidence, I don't see how writing about why other people might care about things you don't value would decrease your confidence or performance.
I think it mirrors the way women might experience a physics class. They might feel like the class is about things that other people value, and that might make them perform worse.
The control group wasn't necessarily supposed to do worse. The control group were ideally supposed to be unaffected.