Why should the Supreme Court decide if a government agency has assumed power not granted to it by Congress? Congress still exists, and Congress can always pass a law kneecapping the agency in question.
Because that's literally in their job description:
> The judicial power shall extend to all cases, in law and equity, arising under this Constitution, the laws of the United States, and treaties made, or which shall be made, under their authority ... --to controversies to which the United States shall be a party;
Because our system is, by default, not one of assuming the government is all powerful and we restrict it here and there, but one where we must proactively add a power.
The Supreme Court is supposed to be a check on the Executive and Legislative Branch? In modern times, the Executive Branch assumes much power not explicitly granted to it and it is the job of the Legislative and Judicial branches to keep it in check.
If congress, doesn't like the ruling, it can reverse it in legislation.