How can I have network sites not use year/month folders by default?

You could just change the option after the blog is created:

add_action('wpmu_new_blog', function($blog_id){
  switch_to_blog($blog_id);
  update_option('uploads_use_yearmonth_folders', false);
  restore_current_blog();
});

Drop this code into a .php file inside wp-content/mu-plugins