It could also fall northwards and take out the CBC building. The Quebec City-Windsor rail corridor would most likely be blocked, as well as train traffic both local (GO, Bathurst Yard) and transcontanental (VIA's Canadian), not to mention freight service. Much of Concord Citiplace would likely be damaged, as would the Spadina Avenue bridge, severing the streetcar lines there as well, isolating them from the rest of the network and the carhouses.
Not good news either way.
Another possibility is that that the hijackers miss the CN Tower entirely and hit Scotia Plaza or the TD Centre instead. Those building aren't nearly as big as the WTC was. I could see wherte the plane go right through it and hit the building across the stree. Taking out the headquarters of a couple of Canada's major banks would have substantial long term consequences for the Canadian economy,