The lawsuit that caused this decision was a ploy by a small corporation to get out of trouble. If you look at their track record, the SEC doesn't really punish large corporations (like Wall Street) very much, if at all, so it getting defanged won't really change much in that regard.
To be more precise about what this case is about, the SEC has two methods through which it can seek enforcement of violations: "civil action", where it files a case with a district court, usually to seek an injunction to stop the violation; and "administrative action", where the case is filed internally and brought to a judge who, while on SEC payroll, is nominally independent from the rest of the process of the Commission.
The second is what's under the lens here, with the accusation being that "administrative courts" are being used to circumvent the Seventh Amendment guarantee of a jury trial in civil suits.
Though there is a second half that may prove much more interesting than agencies merely being forced to play by the rules when it comes to judicial action. It goes further and claims that Congress went afoul of the "nondelegation doctrine" when they delegated powers to the SEC. Specifically, by way of letting them pick and choose whether to use the actual courts or their own courts, Congress delegated a degree of legislative authority to the SEC (the specific reasoning is that tribunals not bound by Article III of the constitution is a power granted by Article I, the article that gives Congress the authority to legislate. think like how Congress can decide to act like a court).
Obviously, this is much bigger, since many other agencies of higher importance may also be in violation of that doctrine. I think it's likely for the Supreme Court to concur with the first half, since it follows directly from the most obvious interpretation of the Seventh Amendment. The second half is… less likely, but still possible. Seeing the Supreme Court declare a judicial open season on practically every three-letter agency would be fun, if nothing else.