I hope this gets resolved for you. I used to work for Geek Squad and there were certain lines that caused us not to be able to repair or replace units. Things like insect infestations or damage due to intention. This creates an unfortunate outcome for some who in my opinion truly deserve the service.
On one hand, the dog is a living being that made an intentional decision to damage the product. You can’t say “my dog accidentally chewed my pencil” because it did it on purpose. It doesn’t fall under normal use and on some degree (on paper) the employees hands are tied.
On the other hand, the Apple Pencil is a low cost item compared to their other offerings. Keep fighting this up to the higher levels and someone should be willing to honor the work. At geek squad we regularly made exceptions to the loud customers because we wanted to keep their business and we also wanted the disruption to stop. It had to be called by a manager but it got done.
Again, good luck in your repair request!