Like I said already: Zunger isn't blaming anyone. He's making a statement of fact. The fact, which is true, is that damore wrote a memo. The fact, which is true, is that having read this memo, many of Damore's coworkers would not be willing to work with him. These are facts. They're not attempts to assign blame or fault, they are objective statements about the state of the world.
As soon as you say the word "justified" or "understandable", you're not responding to Zunger, you're responding to a strawperson. There is no excusing, justification, or blame in the article. There are statements of fact.
You're conflating causality and blame. Zunger only discusses the former, and there is a huge difference between them. You're transforming his statements on causality into ones on blame when they clearly aren't. Damore wrote a thing. That thing hurt people. Cause, effect. No blame. Hawaiian government employee pressed button. A million people were alerted of an impending missile by accident. Cause, effect. No blame. (To be clear, with Hawaii, the blame, imo, falls onto the design of the system, and not the guy who happened to misclick).
In another post you claim that Zunger uses the phrase "it's your fault" (an assignment of blame), But the word "fault" doesn't appear in the essay. Zunger specifically says that Damore's action "has caused a significant harm" to his colleagues. But that, too, is a statement of causality, and is not assigning blame. (I think this is telling by the way: to justify, to yourself, your disagreement with Zunger, you managed to invent things the essay didn't actually say, without even realizing it!)
To be very clear on this, I think that violence is potentially expected in all three cases you mentioned, and justified in none of them. The exact argument Zunger is making works in the reverse, by the way. "You came out as trans to the office, all of whom are staunchly on the religious right and as a result now refuse to work with you. This is...problematic for your employer, and makes you decidedly less valuable from the perspective of your employer. This is problematic.". Am I blaming the trans individual? I certainly don't think so.
Zunger's argument is almost entirely a utilitarian one: You have made yourself less valuable to the organization, and either we get rid of you, or we get rid of a lot of other people. The choice is, unfortunately for you, obvious. And that's the case irrespective of who is "at fault".