The EPA creates laws. Laws, by design, subjugate people. Laws against drunk driving remove your rights and subjugate you to the rule of law. Laws against murder remove your rights and subjugate you to the rule of law. Laws against pollution remove your rights and subjugate you to the rule of law.
As we have learned more about the environment, EPA laws have gotten tougher. We now know that breathing lead is bad for you; hence laws requiring unleaded gas. We now know that breathing mercury is bad for you; hence the laws requiring emissions limits for coal power plants. These laws come directly from the Constitution, which tasks Congress to provide for the general welfare of the people of the United States.
In the future, as we learn more about chemistry, biology and public health, those laws will change again and get more restrictive. There will always be a tradeoff between what is achievable via BACT (best available commercial technology) what is affordable and what gets the most good for the most people. There will be people on both sides of the argument, as there should be - and compromises will be made. But those compromises will absolutely result in laws that subjugate people. (To use your language.)