Congress currently has, and always has had, control of regulatory agencies. There are many ways this works. In many cases, congresses created the agencies by legislation so they can simply change the powers of the agency. If they don’t like a regulation, they can pass a law overriding the regulation. If they didn’t like an agency using chevron a certain way, they can, again, pass a law. They can also withhold monies from the agencies or restrict the use of those monies.
I get that passing laws is hard but that is one of the reasons to have agencies!