Disable author pages for specific users

I think a combination of the answers so far along with an admin area field to disable the author archive(s) is the best bet.

A class to wrap everything up (along with some constants and methods that will be clear later):

<?php
class Author_Archive_Disabler
{
    // meta key that will store the disabled status
    const KEY = '_author_archive_disabled';

    // nonce name
    const NONCE = 'author_archive_nonce';

    private static $ins = null;

    public static function instance()
    {
        is_null(self::$ins) && self::$ins = new self;
        return self::$ins;
    }

    public static function init()
    {
        add_action('plugins_loaded', array(self::instance(), '_setup'));
    }

    // helper to see if the archive is disabled.
    public static function is_disabled($user_id)
    {
        return 'on' == get_user_meta($user_id, self::KEY, true);
    }

    // adds actions and such
    public function _setup()
    {
        //
    }
}

To add fields you hook into edit_user_profile (shows fields on profiles other than your own) and show_user_profile (shows fields on your own profile).

<?php
class Author_Archive_Disabler
{
    // snip snip

    // adds actions and such
    public function _setup()
    {
        add_action('edit_user_profile', array($this, 'field'));
        add_action('show_user_profile', array($this, 'field'));
    }

    public function field($user)
    {
        // only let admins do this.
        if(!current_user_can('manage_options'))
            return;

        echo '<h4>', __('Disable Archive', 'author-archive-disabler'), '</h4>';

        wp_nonce_field(self::NONCE . $user->ID, self::NONCE, false);

        printf(
            '<label for="%1$s"><input type="checkbox" name="%1$s" id="%1$s" value="on" %2$s /> %3$s</label>',
            esc_attr(self::KEY),
            checked(get_user_meta($user->ID, self::KEY, true), 'on', false),
            __('Disable Author Archive', 'author-archive-disabler')
        );
    }
}

Pretty straight forward: only show the field to administrators, print a header, nonce field and the “disable” checkbox itself.

You hook into edit_user_profile_update (others’ profiles) and personal_options_update (your own profile) to save things.

<?php
class Author_Archive_Disabler
{
    // snip snip

    // adds actions and such
    public function _setup()
    {
        add_action('edit_user_profile', array($this, 'field'));
        add_action('show_user_profile', array($this, 'field'));
        add_action('edit_user_profile_update', array($this, 'save'));
        add_action('personal_options_update', array($this, 'save'));
    }

    // snip snip

    public function save($user_id)
    {
        if(
            !isset($_POST[self::NONCE]) ||
            !wp_verify_nonce($_POST[self::NONCE], self::NONCE . $user_id)
        ) return; // nonce is no good, bail

        if(!current_user_can('edit_user', $user_id))
            return; // current user can't edit this user, bail

        update_user_meta($user_id, self::KEY,
            !empty($_POST[self::KEY]) ? 'on' : 'off');
    }
}

Verify the nonce, make sure current user can actually edit the user, then save stuff. if the box is checked, it will go in as “on”.

Now hook into template_redirect, check for the author page and 404 it if it’s disabled.

<?php
class Author_Archive_Disabler
{
    // snip snip

    // adds actions and such
    public function _setup()
    {
        add_action('edit_user_profile', array($this, 'field'));
        add_action('show_user_profile', array($this, 'field'));
        add_action('edit_user_profile_update', array($this, 'save'));
        add_action('personal_options_update', array($this, 'save'));
        add_action('template_redirect', array($this, 'maybe_disable'));
    }

    // snip snip

    public function maybe_disable()
    {
        global $wp_query;

        // not an author archive? bail.
        if(!is_author())
            return;

        if(self::is_disabled(get_queried_object_id()))
        {
            $wp_query->set_404();
        }
    }
}

You can also filter the author link so a disabled user never gets linked to.

<?php
class Author_Archive_Disabler
{
    // snip snip

    // adds actions and such
    public function _setup()
    {
        add_action('edit_user_profile', array($this, 'field'));
        add_action('show_user_profile', array($this, 'field'));
        add_action('edit_user_profile_update', array($this, 'save'));
        add_action('personal_options_update', array($this, 'save'));
        add_action('template_redirect', array($this, 'maybe_disable'));
        add_filter('author_link', array($this, 'change_link'), 10, 2);
    }

    // snip snip

    public function change_link($link, $author_id)
    {
        if(self::is_disabled($author_id))
            return apply_filters('author_archive_disabler_default_url', home_url(), $author_id);

        return $link;
    }
}

All of the above as a plugin