About the best thing I can suggest is if having multiple partitions is an acceptable way to get more use out of the device you might be able to do something sneaky like modify the Disk Label (IE, partition table) on the disk so instead of having a single 250 MB partition sitting on your 2GB SD card you retain the existing 250MB filesystem unmodified and then create a second partition that uses the rest of the disk. (Obviously this will mean you end up with two separate drive volumes sitting on your desktop.) The two ways I can think of approaching this would be to:
A: Use a binary editor to attempt to modify the existing disk label on the volume that you DD'ed over from the ZIP disk, modifying the correct field so the MacOS container "looks bigger", and then use a non-destructive disk partitioner to create the second volume (you'll be digging into some arcane documentation to pull this off), or possibly B:
B: Create from scratch a new disk layout by formatting and partitioning it with the requisite native disk tools. (IE, write the disk label and drivers with the Mac formatter, and then create two data volumes; one a tiny bit bigger than your current filesystem and the other occupying the rest.) Then mount the DD-ed-from-the-ZIP SD card and the new SD card you formatted on a computer that understands classic Mac disk labels (I think OS X still does, another option would be Linux), and then DD the contents of *the data partition your copy-protected program is in* over the corresponding section of the new disk. (IE, we're not DD'ing over the full raw disk, just the actual partition data.) I *think* that might legitimately work. (Unless the copy protection for the program does evil things like caring about specifics of the disk label, etc.) Your mileage may totally vary.
Plan B: My vague understanding is that the SCSI2SD can actually emulate multiple SCSI disk devices at once, does that help you? I honestly have no idea, I don't own one.