I'm about to read the elisp to check, but I'd bet if you added a --version flag that gave the save results as /usr/bin/python, emacs would be happy.
Update
Here's the code in python.el line 1555 et seq in EMACS 23.3.1:
(defvar python-version-checked nil)
(defun python-check-version (cmd)
"Check that CMD runs a suitable version of Python."
;; Fixme: Check on Jython.
(unless (or python-version-checked
(equal 0 (string-match (regexp-quote python-python-command)
cmd)))
(unless (shell-command-to-string cmd)
(error "Can't run Python command `%s'" cmd))
(let* ((res (shell-command-to-string
(concat cmd
" -c \"from sys import version_info;\
print version_info >= (2, 2) and version_info < (3, 0)\""))))
(unless (string-match "True" res)
(error "Only Python versions >= 2.2 and < 3.0 are supported")))
(setq python-version-checked t)))
What it's doing is running a one-liner
from sys import version_info;
print version_info >= (2, 2) and version_info < (3, 0)
that just prints "True" or "False". Fix your script to handle the -c flag and you should be fine.
Alternatively, you could take the hacker's way out and force the value of python-version-checked to t, and it'll never do the check.