An alternate would be to only build a partial wye from the west, which would basically require a station at Honeydale/Cloverdale. The subway would depress in grade into an underground station, and just east of the station there would be a partial wye that would dip under the Milton line, and surface on the south side to access the yard. Not ideal for train movements, but unless there's an option I've missed that may be the only reasonable way to do it.
A partial wye should be adequate. Trains would presumably be sent to the yard immediately after dropping passengers off at the Honeydale terminal station.
I still see Honeydale being an at-grade station, just east of East Mall. For the wye, trains would descend just east of Shorncliffe - there is about 250m to descend, before curving under the CP corridor. The grade and curve can be somewhat tighter than standard, since it is not for revenue service.