Because that’s a Wiccan law- not a witch thing.
Not all Witches are Wiccan.
Even if someone is a Wiccan (or just believes in some form of the rede in their own religion or culture), death is a part of life and if the animal was not killed but passed away from natural causes I don’t see the “harm” in using its skull as a representation of death or rebirth (or to honor the animal or a deity associated with that animal).
That said, I’m not Wiccan and I don’t see anything wrong with killing animals for food and then using as many parts of the animal as possible (including skulls and bones). We have a huge freezer full of hunted deer meat in our garage right now to use for protein through the winter. I’m normally vegetarian but I will eat venison because I am against the environmental problems (and the inhumane treatment) posed by farming animals for meat, I’m not against eating animals that were hunted ethically (ie. not poached or overhunted).
So even if you are normally a person who considers the consequences of your actions and how it will harm others (not necessarily Wiccan but most cultures have a similar “Golden Rule”), you can still use animal parts if they were obtained according to your own ethical standards.