Good catch.  It appears that when Quebec amended the Constitution to eliminate Catholic and Protestant school boards, it used the notwithstanding clause to allow a transitional period of instruction in those two religions - its temporary use being foreseen from the beginning.

Whether or not it's used for a negative purpose is in the eye of the beholder, isn't it?  Ask gays and lesbians what they thought of Alberta's effort to stem the tide of same sex marriage.  

And I understand a lot of Quebec anglophones were pretty unhappy with early versions of that province's language laws.  In fact, that's precisely what gave section 33 such a bad name in Canada.  You know, the kind of thing that prompted that guy to call it "an ugly boil on an otherwise beautiful document."  

It may have been a political necessity, but I wouldn't expect anyone in favour of rights and freedoms to be happy when it's used.