Not to say that I'm leaning towards the conspiracy interpretation, but all those questions have somewhat plausible answers. So let me play the devils advocate here.

Why would boeing go from plainly assassinating somebody, to then trying to kill somebody with influenza b, a usually easily survivable infection for somebody in his age range?

Well if you conjecture that both deaths were indeed a murder then that means Boeing's hitmen just fucked up the oldest trick in the book, making it look like a suicide. Makes sense to switch methods.

Why wouldn’t they just assassinate him too? Everybody already thinks they did it, it’s not like they saved any face by using such an unlikely method.

Plausible deniability. One whistleblower "suicide"? Suspicious. Two whistleblower "suicides" shortly after each other? Very suspicious. They may be an immensely powerful company, but that doesn't mean they are entirely invincible.

And how the hell did they even manage to do it?

Maybe they just saw the victim being in the hospital with a naturally occurring influenza infection and helped an already likely secondary infection along, virtually guaranteeing a fatal outcome? Not sure how lethal MRSA is exactly, but doesn't look all that friendly from a quick Wiki glance.

Again, not that I'm saying this conjecture is true. But the circumstances and the timing of it all are just a bit too suspicious to not at least entertain the hypothesis. I mean it's not exactly statistically relevant, but 2/14 is still a ridiculously high mortality rate for being a Boeing whistleblower.

So people will speculate. Presumption of innocence is a law seldom obeyed in the court of public opinion. That doesn't mean the conspiracy theory is either true or false.