Yes, there's no Internet Config like in the old OS9 days so it is enfuriating to have to use MS software to change a global parameter that Safari uses by default.

I had my FTP helper set to Fetch, and after installing Safari for the first time it retained my preference. Now I have to launch explorer to change the FTP helper for Safari, and there's no third party app to do it - stupid huh?

I checked recently modified files after changing this pref in IE
and the following two files were modified :

~/Library/Preferences/com.apple.internetconfig.plist
~/Library/Preferences/com.apple.LaunchServices.plist

So I'm guessing it might be possible to edit one of these to give
the desired effect - ie. changing the system-wide handler for
FTP.

I'm not expert enough to advise further, maybe someone else
could pick-up here?