Of course, you can deactivate and uninstall the plugin normally. Still, it is essential to remember that if it is inactive, WooCommerce will not know the custom order statuses added by the plugin (statuses start with Mailstep - ).
Orders with an unknown status will disappear from the order list when the plugin is deactivated (but will remain in the database) and reappear when the plugin is reactivated.
If you deactivate the plugin, orders with these statuses will automatically change to Processing status, but the client will no longer receive an email notification. You can modify this default behavior in the plugin settings (WooCommerce → Settings → Mailstep → Uninstall section).
Of course, you can also resolve the situation manually by editing the order statuses in WooCommerce before deactivating the plugin. Beware of resending emails from WooCommerce – if the user has already received such an email as part of the purchase process, you probably don’t want to send it again (in this case, the way to turn off sending it is in WooCommerce → Settings → Emails and settings of the selected email and turn it back on after changing the status).