I wouldn't know where to look for similar cases regarding policy on a leave of absence during Substitution. I know where to find the law, but that doesn't mean that my interpretation of the text in the law is the same as what's being done. (This is just my mind playing tricks on me I think, but I seem to remember a case regarding one of my teachers in elementary school going through something like this on medical, not maternal, grounds. I believe she was given tenure four years after she was employed, regardless of her leave. Or maybe she wasn't, but just didn't make an outcry of it being discrimination. I must have been about 8-10 at the time and didn't think about these things, so the chance is, I am completely wrong altogether.)
It is a simple fact of the matter that these are two laws that isn't very compatible. But which one to look more to? For me, not being a part of either side of this case, I would choose to follow the law that benefits the community more than it benefits the individual. After all, that's what we have rules and regulations and laws for: To benefit the community over the individual.
As far as the discrimination issue I started with, I don't know if we can ever know if that was the case starting this off. After all, I am no psychic and can't read minds, so I don't know the inner-most thoughts of the person making the decision in the first place.