They shouldn't need to pass clarifying language every time a federal agency fails to obey the law. In this case, the agency is trying to arrive at a constitutional way of enforcing an unconstitutional law.
But if we establish that legislation must be passed to correct an agency's illegal interpretation of federal law, that standard will end up being used to allow fantastic expansions of every law.
Part of the brillaince of the ACLU was to support lawsuits in which they seemed to be taking a conservative or moderate stand in order to use those lawsuits to set precedents which would be useful to their radical-left agenda.
As it is, I suspect the courts will allow the FEC ruling to stand, in effect amending the law to make it more constitutional, and to make it harder to challenge the consitutionality of the law.
They shouldn't need to sue either. They aren't affected. Congress creates and can destroy these agencies. They are creatures of Congress.