I like LadyAda's bitbang pin solution, as it would do nothing in the face of "standard" serial port connections on "typical" systems (whatever those are). I don't know how portable it would be, though, and in my mind one of the Arduino's biggest selling points is the cross platform support.
The FTDI bitbang solution would require some Arduino PCB support (or some field expedient "ECO upgrades") as well. If you're going to change the board, might as well just add the jumper and leave the software alone...
Maybe make the jumper small and unobtrusive, like the little solder-bridge type jumpers that don't even require a PTH?
Hmm, on an alternative note, is there some way to disable the handshake pins in the FTDI chip using the FTDI tools?
-j