Of course he'd be told to stop. Not asked, told.
Section 3, Unsportsmanlike Conduct: Possession or use of foreign or extraneous object(s) that are not part of the uniform during the game on the field or the sideline.
A muslim can't use any old towel. It would have to be a prayer rug or prayer mat that was kept clean and "kept holy." Hence, a violation of the rules.