The point is your objection also applies to A Holocaust.
We can't 100% prevent anything; the Constitution could get amended to permit mass summary executions, with enough votes and public support. That doesn't mean it's not worth trying to make that tougher to accomplish.
The way you make that tougher to accomplish is by adding more checks and balances or repealing laws granting excessive authority to the executive. Packing the court would de facto remove an important one. The thing that would help that is a constitutional amendment prohibiting court packing.