I don't recall which pool it was, but I assume you're right in saying it's not the same one. But the principle is the same in that one public pool is allowing a practice of religious observance and not allowing another. As I recall from the article about the church group, they were only denied once the city officials learned they intended to do baptisms at their private function. Are all religious observances forbidden on public property even when that property is rented for a private function? Going to cancel weddings in public locations if there is a prayer involved? how about banning funerals and prayers at public cemeteries?
No it isn't. The pools are allowing anyone who pleases to use their facilities. What they aren't allowing is anyone to use their facilities for religious purposes. The Muslim women are using the facilities to swim, not to practice their religion. The Christian group was using a pool to practice their religion. Whether you agree with the separation of church and state or not, I don't think you can say there's a double standard here.