It's only in the way if they decide to continue the side-of-the-road alignment south to Lakeshore. The EA took into account two different methods of going underneath the rail corridor - side-of-the-road, and middle of the road/mixed traffic. I don't recall seeing that one or the other was chosen.
In any case, yes, the tower is still actively used and will continue to be until 2019 or so. Metrolinx has no plans for them after that date, but the Toronto Railway Museum would like to keep one of the towers once they've been decommissioned - preferably that one.
Dan
Toronto, Ont.