Would you thereby claim (fwiw, you might, and you might even be right about it: I'm just trying to understand if you have a boundary) that extracting the underlying binary code and embedding it in this program with an emulator--instead of laundering it through rewriting the assembly instruction-by-instruction in Python--would be fair game?
If the binary code involved was only the machine code which dealt with the encryption algorithm itself and not any sort of functionality or sequence, then yes. Courts have placed the burden on the program's "structure, sequence and organization".
If one were to take a small sample out of a copyrighted binary which only implemented functionality and had no remains of the creative process behind it, I'd wager they would be in the clear.
That said, I feel like machine code copyrightability is questionable on its face. A packaged binary with resources and assets such as text would be, but the machine code itself is a more complicated issue. Admittedly this would jeopardize libraries, since they don't contain any expressive elements like interactive programs do.
