The notwithstanding clause lets you set aside the rights and freedoms of art 2 and arts 7 to 15. Basically, the fundamental freedoms such as freedom of conscience, of belief, of expression, then the judicial rights against search, seizure, your rights if arrested, etc (but including the right to life and liberty - but this one is already limited by "as exist" in a free and democratic society, which includes the right to conscript in most democracies I know), and the most important for setting aside: The right to non-discrimination based on sex, origin, religion, etc.
Now why would we want to restrict that last one? You implement conscription, bring it down equally on women, LGBT Canadians and members of any faith, I say. They want full equality - no reason not to do their fair share of the killing/dying protection of those rights requires.