I'm not going to say that Boeing had this guy directly killed, but I can certainly see them and their legal team explicitly trying to make his life as hellish as possible until he felt that he only had one way out. Legal threats if you stop proceeding with your case, legals threats if you don't, they want a terrible warning for any other whistleblowers.
Yes the FBI wanted to make an example out of him for the crime of downloading research papers from a service he had legitimate access to. Even JSTOR thought the prosecution was absurd and didn't want anything to do with it.
I'm fully expecting to learn in a decade or so that spez was behind it using his family connections to push out the one person dedicated to keeping reddit from becoming a profit machine.