I think you are making my point. There is no substitute for "being there," whether at work or on the home front. That's why people who have breaks in their careers, for whatever reason, have a harder time advancing and make less money. Think of it like Malcolm Gladwell's 10,000 hours requirement. If you miss a substantial amount of work, which is roughly equated with experience, you are worth less to most employers.
If someone chooses to take parental leave--paid or unpaid--and loses out on experience, there is always a penalty. If you leave work early on a regular basis or are otherwise not available because of family obligations, there is a penalty, just the same as if you work too much, there is a penalty with your family. Society makes women more likely to incur the penalties because of expectations for women. But it's not a particular institution that is creating the problem. There are women who forego families or at least the majority of the day to day of family life and, I'm willing to bet, their careers and salaries end up comparable to men with like experience.
Short of employers or the law treating men and women differently, there is no way to correct this other than a remodeling of societal expectations, which are hard-coded into our culture, if not our DNA. I, for one, do not want to see the law treat people differently based on race or gender or any other immutable characteristic, so I am opposed to anything that would attempt to level the playing field, especially since negative side effects are very tough to gauge.
As to your last point, I would just say that men and women are and should be equal, but they are not interchangeable. There are certain tasks and jobs that men are better suited to, just as there are some that women are better suited to. That said, I am opposed to any discrimination that does not have a basis in merit.
I don't see how that is "making your point" when your attempted point was that perceptions of discrimination are more damaging than discrimination. The example you gave has nothing to do with what your attempted point was.
The scenario you painted isn't the result of direct discrimination from the employer, nor from perceptions of discrimination from the employee.
But it absolutely is unfair, and is the type of thing that one would naturally and justifiably complain about. There are a lot of other factors though outside of mere maternal leave, ways in which our work institutions are set up that are harder on women than on men and ways our cultural perceptions of what women should do is also a contributing factor (and one easily observable across cultures).