http://developer.gnome.org/gio/unstable/GApplicationCommandLine.html#gapplication-example-cmdline2

for (j = i + 1; argv[j]; j++)
  {
    argv[j - 1] = argv[j];
    argv[j] = NULL;
  }

If you're on the last argument (i.e. argv[i + 1] == NULL), you won't get a single iteration of this loop, and the argument won't be popped. I think this simpler loop works correctly:

for (j = i; argv[j]; j++)
  {
    argv[j] = argv[j + 1];
  }

Also, my understanding here is that the arguments as passed are a deep copy. If that's the case, I believe the popped option is being leaked by this code. Shouldn't it g_free (argv[i]) before the loop?