This is the most important part of the article:
The revocation comes two weeks after the Treasury Department slapped sanctions on the founder and editor of USA Really, Alexander Malkevich, making it a crime to conduct financial transactions with him.
It is simply illegal for ISRG (organization behind Let's Encrypt) to provide any services to individuals on Specially Designated Nationals (SDN) And Blocked Persons List:
It also lists individuals, groups, and entities, such as terrorists and narcotics traffickers designated under programs that are not country-specific. Collectively, such individuals and companies are called "Specially Designated Nationals" or "SDNs." Their assets are blocked and U.S. persons are generally prohibited from dealing with them.
It's not the first time Let's Encrypt had to do so - see dnr-online.ru case.