In my ideal world, "mute user" is a protocol reaction, and I have a bot that I configured to mute any user who replies with specific keywords. The bot has a website where I can go and mute/unmute users too.

Dad, geek, entrepreneur. Conversation liquidity provider. vrypan.net (home), @weatherxm (work), @l--o--l (fun). Also https://paragraph.xyz/@purplesubmarine

Would the protocol level mute user just be a Boolean for clients to do what they want with? How would that look on a hub level?

Head of Developer Relations at /pinata | Technical Writer | Building honeythread.xyz | Tinkering Photocaster.xyz | stevedylan.dev/links

I was thinking very high level. But a nice way to do this would be some kind of reaction that clients could honor (or not). 
MESSAGE_TYPE_LINK_ADD already supports this.