No.
OneWorld uses SMB to connect to the Deployment Server. The connectivity is driven through the foundation code, and there is no way to modify how this connectivity occurs.
In my opinion, FTP is WAY more buggy and a security risk in comparison, especially since passwords are sent across the wire in clear-text format. I have disabled Telnet and FTP pretty much across the board with my servers, and use SSH and SCP (which of course is the same port). Nothing is perfect, of course, but the encryption across the wire is certainly better than clear text.
But, to return to the question concerning the deployment server, you will be certainly restricted from use of any development tool - and, of course, the deployment server also contains the central location for the oneworld licenses. It is certainly possible to shut down the deployment server when it is not needed, but you must have the ability to get it back up and running again quickly to get to certain aspects of OneWorld.