You can put it into listening mode and request the ID over Serial USB by pressing the i key. I guess this is more or less the same as the Spark CLI though.
However you probably have to get your PUBLIC KEY and ID sorted with @Dave first. But
Yep, you can flash the Bootloader.bin to address 0x8000000 and the Core-firmware.bin to 0x8005000. I'm not sure if you can get the Factory-firmware.bin and Public Key programmed to external Flash though through the ST-Link though. I've only done this over DFU USB. Check out the process here:
I'm guessing you need DFU for the external Flash since that flash is on the STM32's SPI bus. That said, you can write the data from a core-firmware.bin file much like you'll do for the cc3000_patch_firmware.bin so I'd say it's possible to do it all via JTAG and letting the code run.