“to deactivate single privacy options”
You’ll need to fork the plugin and hack away. I use all options in my installs so removing any is not an option for me.
Edit these labels and blog admins will only see the options you want:
<label class="checkbox" for="blog-private-1">
<input id="blog-private-1" type="radio" name="blog_public" value="-1" <?php checked('-1', get_option('blog_public')); ?> /><?php _e('Visible only to registered users of this network', $this->l10n_prefix); ?></label>
<br/>
<label class="checkbox" for="blog-private-2">
<input id="blog-private-2" type="radio" name="blog_public" value="-2" <?php checked('-2', get_option('blog_public')); ?> /><?php _e('Visible only to registered users of this site', $this->l10n_prefix); ?></label>
<br/>
<label class="checkbox" for="blog-private-3">
<input id="blog-private-3" type="radio" name="blog_public" value="-3" <?php checked('-3', get_option('blog_public')); ?> /><?php _e('Visible only to administrators of this site', $this->l10n_prefix); ?>
</label>
becomes…
<label class="checkbox" for="blog-private-1">
<input id="blog-private-1" type="radio" name="blog_public" value="-1" <?php checked('-1', get_option('blog_public')); ?> /><?php _e('Visible only to registered users of this network', $this->l10n_prefix); ?></label>