Since an agency’s budget is often controlled by either the President or by Congress, and the actual continued existence of the agency itself can be determined by Congress, can administrative agencies ever be truly autonomous?

1.) Since an agency’s budget is often controlled by either the President or by Congress, and the actual continued existence of the agency itself can be determined by Congress, can administrative agencies ever be truly autonomous?
2.) Since environmental protections are a relatively new and unsettled area of the law, is it too soon to use constitutional amendments as a tool to ensure public good? If this route was taken, how would you recommend the new amendments be written, so they respect other constitutional rights?