There is no question that the proper way to go about removal is constitutionally, thru impeachment or within a house of the legislature within their own body.
But, what happens when the system is so corrupted that those remedies are no longer viable?
Imagine if an invading army breached our borders and installed their own congress and POTUS and, yes, even SCOTUS. Now, while imagining that, tell me how the result is currently different.
Your hypothetical President, Congress, and Supreme Court installed by an invading army would not have been elected or appointed under the Constitution. The current President, Congress, and Supreme Court were elected or appointed under the Constitution.
If you believe otherwise, then I am not sure what you accomplish by asking the Supreme Court to also ignore the Constitution.