Mis-understanding "discrimination", again

I've objected, a number of times, on this blog to the use of the term "discrimination" to describe what it is that religious institutions do when they hire-for-mission.  Sure, the word has a meaning which fits.  But, in our public debate, "discrimination" is always "unjustified" or "unwarranted" or "unfair" or "prejudiced" discrimination.  In my view, that which makes "discrimination" wrong is simply not present when authentically religious institutions hire-for-mission. 

That said, here's an article in USA Today, "Case Involves a Collision of Rights:  Calif. Doctors Accused of Using Faith to Violate Law Against Anti-Gay Bias" ("using" faith?) which asks, "When does the freedom to practice religion become discrimination?"  I guess the "freedom to practice religion" never "become[s] discrimination", but put that aside.  Why isn't the answer, "the freedom to practice religion necessarily involves, sometimes, what could be characterized -- but is not helpfully characterized -- as 'discrimination.'"  (I realize that the case discussed in the story is not really a hiring-for-mission case, but more of a conscience-based-exemption case, of the kind Rob Vischer knows a lot more about than I do.)