That's not their call to make. They have no right to host GP's intellectual property and refuse to take it down after being contacted by the rightful owner.
You're not paying any at all. Arxiv did not refuse to take it down. Arxiv did take it down even though they had no obligation to do so. Also, anyone can claim anything online, and it's the timing of papers that ultimately matters.
You have no idea how many emails were exchanged, attempts at explaining them what a commit log is, what verified commits are...to just refuse to do anything until Stanford weighed in.
It is incredibly condescending to say "arXiv is not a place for a copyright strike". as if I decided to start one.
If somebody gets robbed in front of a place of worship/whatever, would you scold the victim by saying that's not the place to get robbed?