The issue with the COVID protocol wasn't necessarily that he broke the protocol, but that he lied to the team about it afterwards.
If you recall, this happened in 2020, when COVID fears were peaking. He (and Plesac) went out for dinner with friends (at the time a breach of protocol), then lied about it and boarded the team plane, thus putting the entire team and its short-term competitiveness into question. Heck - even Plesac said he broke protocol, and the team went out and got a car service to drive him back to Cleveland so he wouldn't have to risk exposing his teammates on the flight.
Remember - positive COVID tests and exposures meant that you were immediately quarantined, and the team had to call up someone from their Taxi squad. With MLB's policies being a very strict "any exposure gets you quarantined" policy, if Clevinger would have been exposed to COVID, that could have put a vast majority of the Cleveland players into isolation, and therefore ineligible to play.
Regardless of hindsight and what we may know about COVID now, looking at the potential consequences involved purely in terms of the impact on the baseball team, that was a stupid decision compounded by a breach of trust. His actions could have taken Cleveland out of the race very quickly.