I think Justin was just trying to make a rhetorical statement about the direction the government of Stephen Harper, rather than it being a serious statement about thinking Quebec should separate.
Moreover, I doubt that he's alone, not just in Quebec, but across Canada. I mean, hell, how many times did certain conservatives imply the West should separate because of the direction of the Chrétien government? I doubt many of them were serious. We make more of a hullabaloo because he's a Trudeau and he's a Liberal.
But, wow, what a stupid way to put it as he did. This will come back to haunt him for sure. He does need to clarify, majorly.