Is that even nessecary? Honestly, how hard is it to open your FTP client, connect to the site, navigate to the directory, right click on it and choose Nuke from the custom commands (assuming you're using FlashFXP). About 5 mouse clicks!
Unless you're using ioBanana, there is no easy way to do this. ioA cannot be run from outsite of ioFTPD, as it relies on ioFTPD's enviromental variables. Same goes for the available nuke Tcl scripts, they cannot be run outsite of ioFTPD for obvious reasons.
You'd need a script to authenticate users (msg bot !nuke user pass /dir/to/nuke). Then proceed to login to the FTP, change to the parent directory and issue the site nuke command. I'm sure there's several scripts for glftpd that would work with a few modifications.
Update: ioA v1.1.7+ can be run outside of ioFTPD.