Yep, I agree. This is a wart in the vanilla python REPL, and org-mode can't really do much about it. Except maybe warn people.
As John noted, this is less of a problem if you use ipython as your REPL. I think it is enough to just do
#+BEGIN_SRC emacs-lisp
(setq org-babel-python-command "ipython")
#+END_SRC
but I haven't tested this extensively since, as I mentioned, I prefer to use Greg Sexton's ob-ipython instead. This integrates with the Jupyter kernel by sending JSON to a web socket, rather than just pasting the source block into a buffer, and that seems to be a more robust approach.
Will