Yes, agreed, the agencies were put in place by executive order and they're being gutted. However, that doesn't mean the executive branch is being gutted. Gutted means "to destroy the essential power or effectiveness of". Maybe there's confusion about the word "gutted"?

Indeed the power and effective of agencies is being dramatically reduced. I believe this is the point that was trying to be made.

However, rulings like Trump v. United States vastly expand the power of the executive branch. Even if you're one of those people who believes in Unitary Executive Theory, prior to Trump v. United States, those powers were hypothetical. Hence the need for a ruling. It's to be seen whether a Unitary Executive would be more effective.