Can the President undo[] ... a law passed by Congress and upheld unanimously by the Supreme Court by issuing an Executive Order?
The executive branch is responsible for enforcing the law. The executive can effectively negate a law by simply not enforcing it. In states that have legalized cannabis use, for example, ongoing federal prohibitions are not enforced except on federally-controlled property such as national parks. This is considered a compassionate relaxation of what would ordinarily be a case of federal supremacy. In political science terms, the executive is an elected political branch of government. People elect one candidate over the other to an executive office with the expectation of achieving a policy goal that may include discretion in enforcing some laws more or less vigorously than others.
While the notion of prosecutorial discretion is meant to provide a certain desirable flexibility, it's obvious that it can be (and has been) used for corrupt, personal, and political purposes. Ostensibly a misuse of executive discretion would be grounds for impeachment. But now as we witness more and more gross abuses of executive power, you can sense how frustrated some Americans have become with both their elected leaders and with the system that seems to allow such abuses with growing impunity.
ETA: However, in this case the extension at the discretion of the President is expressly allowed by the law, which I should have found and read before writing this post. See
https://www.govinfo.gov/content/pkg/PLAW-118publ50/uslm/PLAW-118publ50.xml , Division H § 2(a)(3), which states, "With respect to a foreign adversary controlled application, the President may grant a 1-time extension of not more than 90 days with respect to the date on which this subsection would otherwise apply to such application pursuant to paragraph (2)," and then goes on to state the conditions under which the President could grant the extension.
If so, what's the point of Congress or the Supreme Court?
At the pedantic level, Congress is still needed to actually make the law. The executive has discretion to enforce the laws that exist, but cannot enforce laws that do not exist. But you are not very far off when you point out that the emerging political crisis in the United States seems to be trending toward an absolute monarchy.
By design a court can issue a writ of mandamus to correct what it deems to be an abuse of discretion. Inferior courts have the power to direct officers to compel other officers to carry out their duty. But the Supreme Court famously has no power to enforce any of its orders.
As a practical matter, law enforcement has always had broad discretion to structure a program of compliance with the cooperation of the errant party. For example, Boeing is currently under a deferred prosecution program as part of an effort to correct its lapses in quality and compliance with federal regulation. What almost-President Trump has done is simply agree to
defer enforcement for a determined period of time in order to secure compliance in an ostensibly amicable fashion. This happens all the time in the U.S. in a regulatory context. If my company, for example, is found to be out of compliance with regulation, we are not generally shut down immediately. For all but the most egregious violations, there is usually a deferral of further enforcement while we work with regulators and enforcement officers to return to compliance.