Earlier quoted context omitted.
The problem is that "Deep State" is a loaded term. You could very well argue that the N-word is a historically accurate (and Latin) way to describe African Americans. Instead of using "Deep State", it might be better to say "Agency Directors", if you wanted to use neutral language. "Deep State" is loaded. Of course, its more popular these days to value-signal which side of an argument you're on, rather than appearing…
The second sentence in your post is so alarmingly inappropriate that I can't focus on anything else.
I think the OPs point was “deep state” has a deliberate, highly charged, negative connotation.
Don’t conflate the horrible reality of racism with the historical origin of a racial insult. The OP is merely using it as an example to illustrate how terms acquire meaning through time and social norms. Not excuse their existence.