This idea that putting aside the amount of parental leave candidates took when evaluating them for promotion is somehow "punishing" people who didn't take leave seems like a real stretch to me.

I don't think it'd be difficult to let people enjoy the benefits the company has agreed to provide without punishing them, indeed, this strikes me as the only reasonable way for the company to behave. Ideally, as time goes on, all employees with avail themselves of the full suite of benefits making this discrimination againts those who use their benefits will become moot.