Let religions believe and say what they want to. Violence is the dividing line.
There are two possible responses:
1. Recognition of a nutball faction that needs to be watched and contained, or
2. Whining about "persecution" and evading the underlying issue
If option 2 is selected, there's no need for anybody on the outside to "morally equate Islamic fundamentalism with Christian fundamentalism". In that case, the equivalency will be all too clear.