How to write a SPI flash
Oh maybe load a program through jtag of the mcu and have it do the work.   Bit bang with boundary scan, design your board with a header to hold mcu in reset or isolate spi bus if you have to and program it directly with something like this USB to spi decice (comes with c API for host).

You could order the flash parts preprogrammed from any distributor, you could buy a gang programmer or use the sockets in my link above to program them yourself before attaching them.

If you are doing ict you can do it as part of the test on the end of the line.  For high volume reprogramming I've even seen people make little programming devices you can just plug into your board hit a button and let it reprogram.  The list goes on and on, just depends how you want to handle it.

This shouldn't be too hard with a little planning.