I didn't read it as mocking her faith ...but I see where one could interpret it that way ...but none of us, including OP was there so it's really third hand ...I've sat and watched youngsters in HS PE who are supposed to be running ...and doing anything but running ....and the observation that other PE teachers allow other students to sit out the class is not relevant. But OP you are now adding other new things to your post ...and some things that seem to be poor teaching ...poor teaching is not discrimination ....he might be a jerk and leaving students unattended is a red flag ..but neither you nor I were there ...and some teachers are expected to be two places at once and juggle things wo comment ...if teacher was routinely missing from the scene in gym and no other teachers present I'd say that's a problem to investigate by administration ..a safety issue ..My daughters AP English teacher was there only for start of class ...and routinely covered other duties ....lots of dumb things ...but not motivated by religion.
Challenging a student who is not running then stopping the challenge when the student answers can be taken at least two ways. And it's even possible teacher did not know her religion