You have two questions here:
What exactly is this treaty?
and
Does it really have so much control over anime?
The Treaty of San Francisco they reference is otherwise known as the Treaty of Peace with Japan. Representatives from 51 countries worked together to create this treaty at an opera house in San Francisco, CA. The treaty was ratified by 48 of the 51 attending countries, including Japan, on September 8, 1951. This treaty marks the conclusion of World War II and the world's reorganization of Japan as an imperial power.
As far as its effects on the anime industry, this is merely a joke that J-LIST is making. The treaty has no effect on the anime industry. If you are interested in learning more about the treaty you can read the document itself on the UN Websitepdf.
I followed up with Peter Payne owner of J-LIST about your question and his response was:
It was just a random joke. That’s the treaty that officially ends WWII, so I pretended Japan was required to put dumb main charactors in all future harem anime to balance out the ecchi girls.
His reply in context can be seen here:
https://twitter.com/giraffesyo/status/647764344525053952