That said - in the past the SCOTUS has typically tried not to make massive, sweeping changes, unless truly warranted. And even then, they typically make massive, sweeping changes only in instances that expand rights or eliminate harm. They used to try very hard not to cause undue harm with their rulings.
Think about something like the cases that legalized same-sex marriage: a big, sweeping change, to be sure - but the only "harm" from that change was that some bigots now have to recognize a marriage they would prefer not to (and only in the capacity as a government official, or in that of a public business - they remain quite free to be as hateful as they like otherwise). Even though the change was large, the fallout was quite minimal (despite breathless predictions to the contrary by conservatives clearly arguing in bad-faith).
Sadly the court seems to have abandoned that general principle. This ruling is immensely harmful, not just to the EPA but to the general regulatory state that Congress explicitly created over the years. The fallout from this ruling will be vast, and agencies are going to find themselves increasingly unable to actually regulate anything as they find themselves constantly tied up in court. It's going to cause a lot of very real harm to a lot of people in the country, and we will be feeling its effects for a very long time.
Maybe requiring a 6-3 vote to overturn USSC rulings? But then who enforces that? I don't think Congress could pass that law?