Not questioning the OP's intentions, but a remote vulnerability in most SCTP stacks was published last week: http://pastebin.com/m6863ef05 CVE-2009-0065
edit: needed to review the OSI model.
(I am aware of your credentials so I'm trying to figure out what I'm missing, not trying to be snippy)
FTP would be far worse than SCTP, because you're much more likely to be using it.
I'll admit, my mind jumped immediately to "vulnerability in the kernel! much worse than vulnerability in a web server!", which is exactly the wrong way to think about the problem --- once you've conceded code execution to an attacker, you've conceded the box.
Maybe that wasn't his argument. Thanks for calling me out on that.
Either way, the Linux advisory he cited should have absolutely no impact on your consideration of SCTP.