Disclosure: I work for the architecture firm responsible for the design of this building.
Unfortunately, after years and years of not being maintained there wasn't much that could be done with a majority of the structure. That is, without spending tens of millions of dollars (which people weren't exactly lining up to do). Much of the building was actually on the verge of collapse and it wasn't uncommon for the Reverend to enter his office in the morning to find pieces of the building on his desk that had fallen from above.
To answer your concern about what is being saved, there is quite a lot being saved. Many of the windows are being saved - check out the images from yesterdays HUGE accomplishment of removing a beautiful, two-and-a-half storey transept window completely intact! (Did you see it? It's incredibly impressive). The church trustees were so happy with the result, they hugged the workers and architects. Some of the shingles and stone are also being reclaimed to be used in the design.
I agree, it is sad that this building is coming down, but the majority was past the point of being saved (some of the north wall was actually dismantled by hand.) It's just the reality of it.
But, the good news is that a third of the building is being saved (and restored at a great cost). A retail portion going in on the ground floor will open up the building so that it can be enjoyed from the interior, as well as the exterior, seven days a week by everyone, instead of just once a week by a small group of people.
I promise you that the people working on this care about Hamilton and about this building, and are doing their best to design something that will enrich the city. I hope that by the time the building is finished, you will feel that that has been accomplished.