This may fall into the naive thinking of a layman but is it not as simple as GO and VIA agreeing/guaranteeing to CN that at no time would two passenger trains occupy the two platforms at the same time. So if a passenger train is at a platform as another approaches the second train waits outside the station.
I can't imagine that it would add to much time delay or service interruption and I think it would only be an issue at Brampton (there are other two platform stations but I think most/all of the freight on the line splits off just east of Bramalea..no?).
If hourly two-way service goes only as far as Mount Pleasant, it should be simple for GO to schedule off-peak trains in such a way that there would only be one train west of Bramalea at any one time (peak periods excepted) - the GO schedule provides 14 minutes for a train to leave Bramalea and arrive at Mount Pleasant, where it would require a 10-15 minute layover for brake check and crew positioning. Say if the train leaves Bramalea at 9:00, it would arrive at Mount Pleasant at 9:15, depart eastbound at 9:30, and be back at Bramalea at 9:45 and soon on the Weston Sub. CN would still have effectively a mainline track and long passing sidings to itself (two mainline tracks to itself east of Kennedy Road), plus the track unoccupied by GO as it sits at Mount Pleasant.
Even with 10-15 minutes leeway for delays, only one GO train need occupy the Halton Sub at any one time, with the exception of 6:15 to 8:45 and 16:15 though 18:45 or so, when there would likely be two or three trains operating - say 10/15/30 minute service in the peak direction (depending on how GO wishes to schedule its trains) and 30-60 minute service in the off-peak direction. Even in peak hours, GO can handle some increased demand with local trains from Bramalea (paired with express trains from Kitchener and Georgetown) that wouldn't even touch the Halton Sub if it used the third layover track. There's also room on the north/east side of the station for another freight track.
For 30 minute service, which would really be useful (60 minutes just being okay), the third track though downtown Brampton would definitely be needed - this is work that I would support, though it would be very expensive - utility relocation, widening Centre Street, Etobicoke Creek, Queen Street, Union Street, Main Street bridges, as well as widening the embankment, moving the station (and probably the old freight/baggage house), rebuilding the platform, rebuilding the John and Mill Street grade crossings and associated track and signal work.
