__init__.py shouldn't be considered code, or at least it should be considered differently.
It doesn't make sense to enforce print_function, division on a file that only contains imports, a docstring, and perhaps __all__.
Perhaps a better option would be, don't enforce for an __init__.py file only having some subset of {imports, docstrings, comments, all = ...}?
Another option would be to have a separate --select or --ignore for __init__.py files.