He got got because the user used an Apple ID that was linekd to their real identity, which is one of the things Proton is obligated to provide in cases like this.
Proton says all the time, they are obligated to comply with the letter of the law, so do not store anything identifiable anywhere they’re legally required to provide it. They tell you exactly what not to do, to avoid this precise case. They do not want to provide anything they don’t have to, but they also do not want their company shut down.
Reading the article, it looks like there was barely any warning, because it was the type of turbulance that is extremely difficult to detect. Additionally, it seems the dead man had his seat belt on; he died of, as far as they can tell, a fear heart attack, as the plane essentially fell off a midair cliff, dropping 1800 meters (6000 feet) in three minutes. That’s over 10 meters (30 feet) a second).