Yes, a USB Flash Disk is the same as a USB Thumb drive. You can use EZ Flash 2 and either your USB or a floppy to update bios without having an OS installed.
You can also create a bootable DOS floppy holding Asus AFUDOS and the new bios file and flash it that way.
Since you did not mention your motherboard model, I am assuming that these options are available. This is standard Asus stuff.
You obviously cannot use the "Asus Update" utility for flashing the bios since that runs within Windows.