The rumour that the CN Tower lights change colour based on which Pokemon Go team controls the gym have been floating around since before the game has been released in Canada. However, aside from certain holidays and special occasions, the CN Tower lights do not light up for any commercial products or events.
#CNTower owned by #TeamValor. Coloured by owner of gym. @NianticLabs pic.twitter.com/GKTIdaBfbN
— Sakura River (@SakuraRiver) July 19, 2016
So even though there might be Pokemon battles going on around the tower, the colour of the gym will only change inside the app.