I thought it was law for you to have your animals vaccinated
I couldn't find anything suggesting that it was the law to have livestock vaccinated. I'm also not sure if this would vary from province to province or if that's the sort of law that falls wholly under federal jurisdiction (my suspicion is the latter case, given the regulation you're citing, but don't quote me.)
The purpose of this program is to encourage production of livestock by having farmers report suspected cases of rabies in livestock and providing compensation for rabies losses.
Payments are made to owners for livestock that died or have been destroyed due to rabies. Owners of livestock are required to notify their local veterinarian of suspected cases of rabies. Confirmed cases of rabies must be reported to the Canadian Food Inspection Agency (CFIA) to trigger compensation.
Even if it was the law to have your livestock vaccinated, it's arguably still good public policy to encourage reporting it to the proper authority, in the interest of human health and safety, seeing as many people could conceivably be eating that livestock at some point, or otherwise coming into close contact.
The particular regulation you're citing actually says that the Minister of Agriculture will reimburse the province up to 2/5 of what it spends on reimbursing livestock owners.
You could potentially make up some convoluted theory about personal responsibility, impose harsh penalties on farmers who are found to not vaccinate their animals, and remove the reimbursement policy. You could do all that, but I would recommend becoming a vegetarian.