FWIW, I have a lot more faith in a company that allows its engineers to communicate directly with the public. If there's something in particular that should remain quiet, then that should be handled as such on a case-by-case basis.
Moreover, as others have noted, the EPA is a public institution, and should be answerable to the public.
This is authoritarianism, and nothing else. Control, intimidation, and fear.
The EPA functioned fine with Obama. Trump just doesn't want to be answerable for what he knows are unpopular policies.
He didn't win a majority of the vote, it's on his mind (he feels obliged to explain this with paranoid conspiracies regarding immigrants). He knows that what he does is going to get pushback from the public, and he doesn't want it.