This is a dangerous assumption. There is a far greater need for wildlife crossings along the Peterborough route.
As for the alignments
The CP ROW can have tracks added to handle all freight through here, leaving the CN ROW for HSR. A small taking through farmland is neaded east of Trenton to ease a curve.
This is one of the trickier spots, for which a shallow tunnel under public right-of-way probably makes the most sense.
The CN right-of-way is pretty straight here for HSR. The problem is that not all freight can be removed from this corridor. Belleville has a significant yard which is not accessible from the alternative CP right-of way, on top of the CP right-of-way being not very wide and thus even 2 tracks is a tight fit when 3 are probably needed for capacity. A solution whereby 2 HSR and 1 freight track run through on the CN ROW might work, with appropriate protection to guard against freight fowling the HSR track also installed.
Just bypass. There are trickier spots between here and Kingston. I would suggest that Napanee is where HSR should leave the lakeshore corridor, with a local connecting train providing service to Kingston (and Brockville and Cornwall).