Both Norton and McAfee make pretty good products for malware detection on the Mac. Better, though-if you have a backup which you *know* is good (read: not infected, definitely comes from before the hacking event) is to restore that, and then change all of the passwords, etc. which made you vulnerable in the first place.
To answer your original question: ssl would not likely have protected you from this attack. From your report, the attacker got in through FTP using some form of password attack (probably a dictionary), and then proceeded to make merry in your filesystem. Since you appear to now be a target, you might consider making a serious password policy for your office (minimum length and complexity, regular change intervals (monthly, quarterly, something), and stuff like that.
Most security is personal-we give out passwords to people we shouldn’t trust, or use easy passwords because remembering hard ones is a pain (and be clear that I am no different in this regard-my “password discipline” could be lots better :-). Guarding against that kind of thing requires institutionalized vigilance of the kind practiced by outfits like the military. (I worked for them for a while, and while I hated choosing new passwords every 60 days, I admit it enforced security in a way I would not have done).