Yes, you are being too cynical. There is no way that anyone who chose to work at 18F - a place that exists to make government actually more efficient, that has a reputation for quality and execution, and that doesn't pay nearly as well as the private sector - is at all okay with Musk's slash-and-burn version of "efficiency". This kind of message exists to point out the difference: if you actually care about efficiency and good governance, you wouldn't possibly dream of firing these people. Hanlon's razor can't even explain it; even if you're an absolute moron you wouldn't do it. The only possible explanation is actual malice.
No, you can explain it without actual malice. All it takes is Musk having no clue who these people actually are, and not taking the time to find out, because he's got a whole government to go through, so he can't take the time to actually look at any department.
But it isn't easy to tell the difference between that kind of no-time-to-check recklessness and actual malice, at least in any one instance. (You might be able to tell statistically, at the level of the whole government. Not with any one department, though.)
But it's just as destructive as actual malice, so maybe it doesn't matter whether it's malice or not.