If that is an important factor for you, I would lean towards faith based schools (Pepperdine, Oral Roberts, Liberty, Dallas Baptist, Baylor, Samford, etc.)
I am sure there are many other schools with Christian coaches (heck, I think they are all praying for wins every weekend
) but it may not be apparent until your son is on official visits and can visit with players about the coach to find out more about his demeanor and character.
Another thought ... sometimes it is good for your son to be a "light" in the baseball program, sometimes you can have the greatest impact on others when you are "walking the walk" and leading by example.