The Serial Download/Reprogramming mode is usually used when the QSB is in device mode, so I don't think it will be able to load things from the usb stick in this mode.
How come you don't want to use the uSD slot for booting? ( at least loading uboot and the kernel )
Depending on what you are working on, there are ways to boot across a network connection for easy development on a host ( using tftpboot for kernel and nfs mounting for rfs ). Or you could load uboot and the kernel from uSD and load the rfs from nfs. Or you could load everything from uSD and nfs mount a disk on your host or use dropbear for easily transferring userspace programs to the QSB.
Sorry, I'm giving you a bunch of options, because I don't know how familiar you are with linux development, excuse me if I mentioned things you already know of. :smileyhappy:
Regards,
Randy