No. In the end, the execution really is all that matters. Jojo Rabbit is a comedy movie about the Holocaust in Nazi Germany, and the Good Place is a comedy TV show about moral philosophy. Both work because of their execution. No matter how iffy the subject is, the proper execution can make it work.
D&D/Pathfinder could absolutely include a Tefillin/Phylactery magic item useable by Clerics without it being problematic. Or just list a Tefillin as an option for a holy symbol. That would almost definitely be way less problematic than appropriating the item to be used by a Lich for evil purposes.
The line of acceptability is dependent on the execution, not the content itself.