well looking it over more carefully, the plan is ambitious just like the rest of the projects which is good.
the area is almost 10,000 sqaure meters so a lot can be done on it. keeping low-rise (3-4 storey) on queen would be best to make it fit in a bit more with the streetscape as there are lovely old buildings on the south side of queen. and then the high rise building will be backdrop for them. it would be good to have these 2 contrast to give it the greatest effect to give that sense of foreground and backround.
if you're going to work with sightlines for one church, you might as well do it for the other spire as well which is also close by.
when i was doing a study for this area, for a project at school, we decided to use this area for ryerson. what he thought would be best is to put a medical complex consisting of medical reserach and nursing facilites if ryerson ever went that way and expanded their program (much like UofT). so that would be a joint venture with st. mike's hospital. on top of that student residences and lecture halls for the life sciences program would be located there as well. but i can see that being any form of residential as u have mentioned.
the green courtyard is nice as it continues the flow of green space along queen which includes the green space between bond and church on the west and moss park on the east. this should definitely be a public courtyard which can be the entrance for many shops on the interior.