When people say, "The Deep State", what they really mean is, "unelected lifelong government employees who can create regulations that have the force of law".
And that is a problem. Congress makes laws, not government agencies like the FDA, EPA, USDA, etc.
We've seen a near-total abdication of responsibility from Congress on highly charged matters that'll piss off someone, somewhere in their constituency, because they'd rather allow the President to make an Executive Order, or a bureaucrat somewhere to create a rule or regulation that will have the same effect.
It's disgusting, shameful, and the American people need to do better, frankly. We need to demand Congress do their jobs.
So many of our problems can be solved if these people weren't concerned about being re-elected. Elected positions are supposed to be something you take time out of your life to do for a number of years, then you go back to your livelihood - not something you do for the entirety of your life.