In other words, it was written with no consideration for performance at all.
A competent engineer would use Rust or C++ with an in-process git library, perhaps rewrite part of the git library or git storage system if necessary for high performance, and would design a fast storage system with SSDs, and rate-limit slow storage access if there has to be slow storage.
That's the actual problem, LLMs are seemingly just adding a bit of load that is exposing the extremely amateurish design of their software, unsuitable for being exposed on the public Internet.
Anyway, they can work around the problem by restricting their systems to logged in users (and restricting registration if necessary), and using mirroring their content to well-implemented external services like GitHub or GitLab and redirecting the users there.