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

if ( get_option( 'uploads_use_yearmonth_folders' ) == true || get_option( 'uploads_use_yearmonth_folders' ) == '' ) {
      switch_to_blog($blog_id);
      update_option('uploads_use_yearmonth_folders', false);
      restore_current_blog();
}

add_filter( 'option_uploads_use_yearmonth_folders', '__return_false', 100 );