Program Arduino Mega Adk on linux
You can use Eclipse, along with AVR-GCC and AVRDude and an AVR plug-in for Eclipse. Debugging may be a little painful since you don't have all the tools that Atmel Studio gives you. I'd question your employer if you aren't allowed to use the best (free) tools even if they do run on Windows.

Really all you need is the avr-gcc and avrdude to write software for it, you can use any text editor (although it isn't really convienent).  Seems like they are pigeon-holing you into a difficult job. Good luck.