I hear you -- Arduino does have its benefits
I think we're pretty close on the ISO protocol as-is... I don't have a problem with porting existing code in either though. I'm pretty adamant that we need to use the UART provided by the chip for reliable comms though, based on other projects I've worked on in the past. (Yes, you probably can get there if you work really really hard, but it's totally not worth it.)
GCC+AVRDude would be my first choice, actually. Arduino does some very basic stuff for you in the bootloader and API, but nothing that wouldn't take just a couple of days to implement on another AVR yourself.
Honestly, I'm all for Arduino+327 just to see something work.