Yes — a larger CF card can work for the EOS-1Ds firmware update if it is formatted by the camera to a 2 GB FAT16 partition. One reported successful update used an 8 GB Transcend CompactFlash card after formatting it in-camera so the camera saw a 2 GB FAT16 volume.

So you likely do not need to find an old small-capacity card, provided the larger card can be formatted in a way the camera accepts for the update. The key point is not the physical card size alone, but that the camera can access the firmware file from a compatible partition/format during the update.