Have you considered using WebDAV as a replacement for FTP?
The WebDAV protocol can handle recursive deletion of directories on the server, which makes it much faster than deleting in FTP (*).
WebDAV can easily be encrypted by using HTTPS instead of HTTP.
WebDAV has native client support in some operating systems, thus a client is not needed. Unfortunately, the native Windows versions are not that good. Windows support two clients: Web Folders and WebDAV mini redirector.
A WebDAV server can be mapped as a standard drive on the client, and you can simultaneously upload and download multiple files.
A WebDAV client can connect to a WebDAV server from behind a restrictive corporate firewall since the firewalls are typically setup to allow HTTP traffic, but not FTP traffic.
(*) Deleting recursively on the server must also be supported by the client. As an example, the Total Commander WebDAV plugin is just as slow as the FTP plugin as Total Commander is doing a recursive check before deleting.