It's not the job of places of learning to give way to superstition. Indeed, quite the reverse: the whole Enlightenment Project was about bringing light into darkness, and all the Academia I'm familiar with puts itself broadly in the Enlightenment tradition.
So yes, this answer will read as uncompromising. Because, from experience, I've found that rigorous education is incompatible with compromising that rigour in favour of molly-coddling someone's religious beliefs.
There is no sane middle ground. If you're going to start compromising the quality of your teaching to avoid offending someone's belief, you'll quickly find yourself running out of space. Someone's going to get offended that you're teaching males and females at the same time, sat next to each other. Someone's going to get offended that anyone's drawing the human figure, let alone that they have to. Someone's going to get offended that you don't mention their pet crank theory alongside science as if they were somehow of equal merit.
If a particular course's actions are in contradiction to a student's religion, then there are two routes here. If the student is legally a child, then the student completes the actions - they are under the school's guardianship when in school. If the student is legally an adult, then they have the problem, and it's not fair on any of the other students that they should make their problem, the institution's problem. They can either fail that part of the course, or they can do the work.
If a student's beliefs contradict knowledge, science or art, that's not the problem of the place of learning. That's the problem of the student.
If this is about children, then the responsible adults are guilty of abuse, for bringing that state of affairs about, and the school should do as much as it reasonably can to make amends for that failure. Note that I am not saying that a religious upbringing is necessarily abuse. I am saying that teaching children nonsense such as creationism is abuse, because it can cripple that child's future opportunities.
If this is about adults, then they've taken responsibility for failing that part of their education, and should be marked down accordingly.
This has been something of a hot topic in Britain recently, where the teaching of creationism and other ignorances is on the rise, where state-funded schools have been breaking equality laws by selecting staff on the basis of gender, sexuality and religion, and where pressure has been put on educational establishments to subvert the teaching of several branches of knowledge, including the censoring of some exam questions on evolution, and the censoring of two university atheist society's display of the Flying Spaghetti Monster and of "Jesus and Mo" t-shirts, because these were inconsistent with some extremist religous interpretations.
Academia is the bulwark against ignorance and superstition.
I'm not saying that religion = ignorance and superstition. Creationism = ignorance and superstition. Refusing to draw the human figure = ignorance and superstition. Avoiding listening to or playing music = ignorance and superstition. Preventing females from being educated = ignorance and superstition.