@sferik, I read that explanation and although it is a very fancy article with a nice Latin quote, I learned in my Historical Linguistics class in college that the confusion over this phrase is due to an older meaning of “proof” (meaning “to test” rather than “to confirm”). Thus, “the exception tests the rule.” Words change their meaning all the time, sometimes in subtle ways, sometimes in glaringly obvious ways (as anyone who has read a book from a few decades ago that uses phrases like “Shelia was carefree and gay” very well knows). As another example, the word “meat” used to refer to all food, instead of just animal flesh (you get a sense of that older meaning in the word “sweetmeat”).
I tend to believe things I read in textbooks more than things I read on the Internet, but I’ll look into it a bit more, in the interest of open-mindedness, and report back what I find.
And @bpeoples, I think people definitely use this phrase sarcastically now, which only speaks further to how language is an ever-evolving, shifting thing. It works pretty well in that sense too!