Congress can actually legislate the right of agencies to interpret the gaps in the laws back into effect - by passing a law that explicitly gives agencies this power. Just like congress can legislate abortion laws rather than leaving it to judicial precedence. Fundamentally there’s nothing wrong with the position of supreme court to push the responsibility of lawmaking back on congress.
For 40 years, legislation was drafted under the assumption Chevron deference was going to be used to interpret the text of the bills. Now, all of those laws mean something other than what the authors intended.
If this was software, it'd be the equivalent of changing post-K&R C language semantics in a backwards incompatible way, and just saying "Well, if programmers care that industrial control systems are literally burning factories to the ground, they can just fix all the software that was written since 1984. Also, moving forward, we reserve the right to keep making intentionally-breaking changes to the compiler, so during the rewrite, they should take future planned-but-currently-secret semantic changes into account."