Some mitigations may need to come from outside of Tor -- things that make the Internet as a whole more stable, harder to eavesdrop on, and harder to selectively disrupt.
It's very common for sites to use third-party blocklists, and all those lists compete on number of blocked addresses so they all include tor. So lots of sites are not accessible through tor. I'm glad if arxiv is not one of them, though it sounds like their blocking system is a bit overprotective.
I wish these sites would just give read-only access instead of blocking access to content.