Swipe settings in El Capitan Mail.app
I'm going to go out on a limb and say there is no hidden setting to do this. 

I tried making a new user account and switching the primary language to Arabic - so that the text and mail panes are laid out right-to-left instead of left-to-right and the swipe gesture is still:


swipe to right marks as unread/read
swipe to left is trash


My thinking is that if there was an allowance for differing behavior, Apple would have implemented that change in the swipe for languages with right-to-left text flow direction.

I could be wrong and hope someone posts a better answer if I am actually wrong in my guess. My thinking is you'd want to file a bug report to ask for the change if you don't think Apple will re-evaluate this design choice on their own accord.