Force/Override/Set Permalink Structure in Functions

This function will set the permalink structure for your WordPress blog, and it will override the Permalink Settings in the WordPress admin -> Settings -> Permalinks.

/**
 * force set permalink structure
 */
function smartest_set_permalinks() {
    global $wp_rewrite;
    $wp_rewrite->set_permalink_structure( '/%postname%/' );// you can change /%postname%/ to any structure
}
add_action( 'init', 'smartest_set_permalinks' );

Usage

If your theme or plugin needs to force override the Permalink Settings that are set in WordPress admin -> Settings -> Permalinks, you can use this function, while still giving the user some control. Add a checkbox option to your theme/plugin options that allows them to stop forcing the permalink structure. Then do something like this:

function smartest_set_permalinks() {
    global $wp_rewrite;
    $wp_rewrite->set_permalink_structure( '/%postname%/' );// you can change /%postname%/ to any structure
}
/**
 * force set permalink structure only if not disabled by user in settings
 */
if(get_option('YOUR_CHECKBOX_OPTION_KEY_TO_DISABLE_FORCING') == 'false') {
     add_action( 'init', 'smartest_set_permalinks' );
}

In the function above, replace YOUR_CHECKBOX_OPTION_KEY_TO_DISABLE_FORCING with the key of the option in your theme/plugin that allows them to stop forcing the permalink structure.