CN & CP already have several agreements in place to operate on each others tracks in certain sections so its wouldn't be unusual for them to share track instead of having separate mainlines. For example from Toronto to Sudbury(and beyond) both of their lines are single main track(with sidings for train meets). To increase capacity, they entered into an agreement many years ago where trains from both companies would run northbound trains on CP's Parry Sound subdivision and southbound trains on CN's Bala subdivision. I'm guessing CP's got to give something back to CN since the northbounds are primarily empty verse the loaded southbounds using CN's line, meaning greater track maintenance cost.
The southern connection is located at CP Reynolds/CN Boyne where both lines run side by side. This is located about 3 miles south of Parry Sound specifically at coordinates 45°19'8.84"N 79°59'26.17"W
It's tough to see what it looks like on because of a lack high resolution aerial images of the area but its basically a set of crossovers just like your standard "controlled location" with this track arrangement;
For nearly a 100 miles they operate this way until the St Cloud interlocking, at coordinates 46°23'2.99"N 80°48'46.34"W
Where the two lines cross over in the middle there is a bridge, no connection.
They have several other agreements across Canada, see
here.
That said, there are a number of problems that stand in the way of having such an agreement here.
GTA map of existing mainline tracks;
Access to CP's Toronto Yard would be problematic. At points A & B each lines cross over the other on bridge structures and there are currently no connections between the two. However the area surround the two locations are only lightly developed, so I don't think building a new connecting track would be a big issue. CP would probably be more concerned with the operational inefficiency of having to travel away from the mainline to access the yard and with how both west and eastbounds would then enter the yard in the same direction. Though that's certainly by no means insurmountable, as you can see this is how CN's Mac yard is arranged for instance. Though the amount of tracks they have available would have been cut back if the rumored ML purchase of the northern section(A & B) of the yard is correct(
http://urbantoronto.ca/forum/threads/pickering-airport-transport-canada-gtaa-proposed.4855/page-21)
Of course all that is a non-issue if CP's yard is rebuilt elsewhere.
The biggest problem is item C which is probably already the busiest section of track in Canada in terms of total tonnage. Both CN's east-west traffic and north-south traffic(off the Bala) have to run through here to access Mac Yard. It's the one section where two tracks would definitely not be sufficient for both CN & CP. And the line runs through a heavily populated section of Richmond Hill. I'm sure there will be some push back from the community from dramatically increasing freight traffic levels from their already high levels through here. If it was something the freight companies decided together by themselves there's probably little the community could do to stop it. But the effort is being spearheaded by governing authorities which makes it a different story.
Item D, where the Halton sub crosses over the Humber would require a new bridge span for a second track and an expansion of the embankment leading up to it, which is probably the largest rail embankment in the GTA in terms of fill, it quite the view going over that.
What I'd propose is a connection be made to CP's Mactier sub off the Halton for CP traffic here.
The Humber bridge and embankment would have to be widened either way. The new connecting track would require a new embankment and a grade separation over Islington Ave. CP's existing Mactier sub main track would need to be moved to the north side of the corridor while the connecting track would gradually decrease in height from Islington to Steeles at a 1% grade (20 feet height over 2000ft length) which is not much more then the existing grade on the Halton approaching the Humber from the West at a 0.6-0.7% grade. The concrete embankment section would be much like GO's Snider crossing;
It would certainly be cheaper to build the 407 bypass then build additional infrastructure to support expanded GO service on the Milton & Kitchener lines but I'm not sure the same can be said in getting CP off the North Toronto/Belleville(Midtown corridor) when adding all the costs of building new infrastructure, buying the corridors off CP and then relocating CP's Toronto yard. Without the yard relocation it might be cheaper, but its a much tougher sell to CN & CP and there's the Richmond Hill NIMBY issue.
Edit*
For the record I'm completely in favor of seeing CP & CN get "kicked off" all those lines, just providing information regarding the stumbling blocks.