I think Gnu Readline uses standard output for echoing input, prompts, controlling the cursor, etc. You can already see this by redirecting to a separate terminal. In Linux:

$ python > /dev/pts/2

So I think your assumption is not valid. Perhaps you can redirect standard error instead? (python -i . . . 2> output.txt, at least in Linux.) Or maybe use some terminal logging program, like the “script” Unix command. But I’m not sure there is a good use case for enabling Readline without a terminal to output to.