Just to be clear, you have two tickets

Revenue YOW-YYZ

AP ZRH-YYZ(stop)-YVR (and presumably a return somehow)

First of all, the supervisor is correct in that you're SOL if you miss the connection, but that's not because of your not meeting the MCT. It's because you're on two separate tickets, and AC claims it has no obligation to passengers in this situation. Therefore, it's in your best interest to take as early a flight as you can to YYZ to avoid canceling the return flight. You may be lucky in that you could find an agent who will assist you in YYZ if you misconnect and only charge you the same-day change fee (or nothing at all), but it's unlikely.

If, however, that is the only flight to YYZ that you can take, your best bet would be to attempt doing a same-day change in YYZ. I'm assuming ZRH-YYZ is on AC J, which entitles you to concierge service on that leg, and presumably, YYZ-YVR, as part of an international J ticket, would also entitle you to concierge service. There's a good chance they wouldn't give it to you though (the traditional belief was that you only get it on the international portion of your trip; however, Ben L said that it was on all legs).

So, with that in mind, this is what I would do:
1. Take an earlier flight to YYZ or
2. Switch the date of the YYZ-YVR flight or
3. drop the YYZ-YVR flight from your booking entirely and fly it on a revenue ticket (i.e. open-jaw ZRH-YYZ//YVR-XXX-ZRH) or
4. Ask at YOW to same-day change the AP reward ticket to a later YYZ-YVR flight
5. Call the concierge in YYZ to ask them to same-day change the AP reward ticket to a later YYZ-YVR flight
6. Pray your YYZ-YOW flight arrives at the gate on time.