how to deactivate a plugin without using a WP function?

The simplest way is probably renaming the plugin file or folder.

But if you’re trying to handle it directly from the database, you’d have to grab the ‘active_plugins’ value from the wp_options table, unserialize it, remove your plugin from the array and reserialize it and update. You don’t necessarily have to use update_option.

You could also look into a command line tool like WP-CLI. With that installed, deactivating a plugin is a simple command from the BASH shell, like wp plugin deactivate plugin-name.