To me, when people say that the Constitution is "not a suicide pact," they mean that anything that can be enacted by one Congress can be undone by a future Congress. It's been a long-standing tenet that one Congress cannot bind a future Congress, that is, Congress cannot pass a law saying that the law is irrevocable.
The only way to "bind" future Congresses is by amendment, but even amendments can be repealed by future amendments. However, it's the states that ratify amendments, not Congress.
Congress has never abolished an inferior court, but most scholars believe that it has the power to do so. I would think that realigning the courts would be a more likely action. Still, whatever Congress does must satisfy the "necessary and proper" clause in Article I Section 8:
To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution in the Government of the United States, or in any Department or Officer thereof.
Congress would have to show that abolishing a court is "necessary and proper" in the current circumstances, and does not violate other powers in the Constitution. Conversely, Congress would have to show that any new encumbrances or constraints are also necessary and proper and also don't violate other powers granted in the Constitution.
-PJ