This python script allows you to change the unity/gnome keyboard settings for swapping the meta (windows) and alt keys. Should work with Python 2.7 and 3.2

key_swapper.py

#!/usr/bin/python
# This python script allows you to change the unity/gnome keyboard
# settings for swapping the meta (windows) and alt keys. Should work with
# Python 2.7 and 3.2

from gi.repository import Gio

class KeySwapper:
    SWAP_ALT_WIN='altwin\taltwin:swap_lalt_lwin'

    def __init__(self, quiet):
        self.settings = Gio.Settings.new("org.gnome.libgnomekbd.keyboard")
        self.quiet = quiet

    def inspect(self):
        print(self.__get_options())

    def enable_swap(self):
        options = self.__get_options()
        if self.SWAP_ALT_WIN not in options:
            options.append(self.SWAP_ALT_WIN)
            self.__set_options(options)
        if not self.quiet:
            print("enabled")

    def disable_swap(self):
        options = self.__get_options()
        if self.SWAP_ALT_WIN in options:
            options.remove(self.SWAP_ALT_WIN)
            self.__set_options(options)
        if not self.quiet:
            print("disabled")

    def toggle_swap(self):
        if self.SWAP_ALT_WIN in self.__get_options():
            self.disable_swap()
        else:
            self.enable_swap()

    def __get_options(self):
        return self.settings.get_strv("options")

    def __set_options(self, options):
        self.settings.set_strv("options", options)


if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser(description='Changes the Unity/Gnome keyboard configuration for key swapping of the left meta and alt key.\n With no argument the configuration gets toggled.')
    parser.add_argument('--enable', dest='swap', action='store_const', const="enable", help="Enables the key swapping")
    parser.add_argument('--disable', dest='swap', action='store_const', const="disable", help="Disable the key swapping")
    parser.add_argument('--quiet', dest='config', action='store_const', const="quiet", help="Mutes any output")

    args = parser.parse_args()
    quiet = args.config == "quiet"
    key_swapper = KeySwapper(quiet)

    if args.swap == "enable":
        key_swapper.enable_swap()
    elif args.swap == "disable":
        key_swapper.disable_swap()
    else:
        key_swapper.toggle_swap()