As long as it is in the context of an academic or philosophical discussion, I (personally) see no problem with it. It is the spirit in which the discussion is framed that matters.
As Kintama points out, some aspects of "religion" are interwoven into the fabric of MA. (BTW, Buddha would turn in his grave if he found out that someone went and created a religion out of his teachings). Shinto is based on animistic spiritual beliefs, and the line between religion and spirituality is a fine distinction.
(Most) MA can be practiced with and without being subsumed by its underlying religious and spiritual influences. However, difficulties can arise when reconciling staunch religious beliefs and convictions, which conflict with such influences.
Because a subject is taboo, it doesn't mean it should be swept under the carpet and ignored. People have a choice to exclude themselves from the discussion and as long as the discussion remains civil, I see no reason to exclude it - unless such discussion is an afront to their religious convictions.
Personally, IMVHO, I believe that the spiritual influences are more important than learning a bunch of physical techniques.
But then again, I reserve the right to be wrong.