At $100 USD the SAM-ICE for JTAG connectivity isn't particularly expensive. And there is always a serial connection. The actual SAM-BA protocol implemented by RomBOOT isn't particularly complex. I've used a variety of SAM-BA application versions over the years, the newer ones have become less easy to use/modify, and have never been particularly robust.
Personally I'd favour using a serial flash device to plug-in and payload code onto a blank 9260 board. ATMEL demonstrates this with their dataflash on an MMC footprint. On subsequent chips one could use a sub $10 USD SD/MMC Card to payload a boot image onto the NAND. If updating/controlling cards is an issue in production, use a simple bootstrap to pull full images via ethernet from a server.
The "getting started" application would be a particularly good example of injecting run-able code into SDRAM and running it from SAM-BA. Pretty much a case of installing GCC and GNU Make, and running make. I believe the current download for the board contains Keil and IAR examples too. Rebuilding SAM-BA applets should also be a matter of using make, in a similar manner as building AT91BootStrap. Generally the biggest obstacle with the 9260 is the small SRAM.
http://atmel.com/dyn/resources/prod_doc ... oc6297.pdfhttp://www.atmel.com/dyn/resources/prod ... oc3257.pdf