Being willing to kill someone as a “last option” and wanting to kill everyone who poses the slightest threat are not the same motivations.
Also thinking about it, how many people at a company the size of Boeing become a threat by being bothered with criminal practices violating safety and other law and ethic standards? How many do we not hear about because the “normal” coercion tactics work?
Having half your engineering department wind up dead because they raised concerns about issues with the production could backfire much more to begin with, but also it would make every engineer look for a different employer quickly. So trying to destroy someones reputation first, ousting him, creating a “him vs. us” mentality is preferential. It also makes it easier for the company to move on after killing him, if the need arises.
So both from a emotionally crippled, but not fully devoid point of view and from an completely psychopathic cold blooded strategy point of view it makes sense to not pull the trigger on everyone right away.