All the maintainers for linkerd are employed by Buoyant, which means under current graduation criteria it wouldn't have been graduated in the first place. Will be interesting to see if the CNCF TOC does anything about it though.
To my knowledge the CNCF has archived projects [1] before for one reason or another (most commonly inactivity), but I'm not aware of a case where they have actively kicked a project out.
It's also interesting to think about what that would even look like since part of the project being added to CNCF in the first place were the trademarks etc. got handed over too [2] - not just the code.