You can just delete the plugin and it will be deactivated. But just to make sure you also don't call up a cached version of the website, make sure you also delete the following files from FTP
- [wordpress]/wp-content/advanced-cache.php
- [wordpress]/wp-content/cache
- [wordpress]/wp-content/db.php
- [wordpress]/wp-content/object-cache.php
- [wordpress]/wp-content/w3tc-config
This will delete all the cached information from your website, but also your W3TC configurations. If you want to re-enable the plugin at a later stage I'd recommend you move them somewhere out of (WordPress) sight an put them back again when you need them again.