Well, I found the following solution, by not using emacs-for-python and activating flymake on load of Python files with the 'find-file-hook:
(when (load "flymake" t)
(defun flymake-pylint-init ()
(let* ((temp-file (flymake-init-create-temp-buffer-copy
'flymake-create-temp-inplace))
(local-file (file-relative-name
temp-file
(file-name-directory buffer-file-name))))
(list "pep8" (list "--repeat" local-file))))
(add-to-list 'flymake-allowed-file-name-masks
'(".py$" flymake-pylint-init)))
(add-hook 'find-file-hook 'flymake-find-file-hook)