I think the chances we will ever see the CNR mainline rerouted out of the city is virtually nil. Surveying, land acquisition and construction costs would realistically run into the hundreds of millions of dollars and who would pay for this? Not CNR. Why should they? The current alignment works just fine for them. It's only a pain in the ass for motorists in the downtown core whenever they have to wait for a 150 unit train to pass by, and that only happens several times per day.
An argument could be made on the basis of safety and liability concerns if there were ever a major derailment. While such a disaster is possible, I'm sure CNR is extra vigilant about track maintenance in built up areas, and speed limits in the city are lowered, so a derailed train would not have as much momentum as it would in a rural area.
The only was a new alignment will become a priority is if the province mandates it, and if they did, I imagine there would be an expectation that they would have to subsidize the cost of such a venture.
There would be costs to the community if the tracks were realigned. The passenger station would no longer be downtown. There are also a number of spurs to industrial areas in the city that would have to be maintained, or, if abandoned, then alternative transportation of heavy goods to the companies supplied by these spurs would have to be arranged (improved highway and street infrastructure).
I don't see this ever happening.