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We are currently deploying units with the ATMEGA328 chip. Currently, all ICs have been flashed using the Arduino IDE. Upon release, we would like to offer updating of firmware in some cases, but obviously we would not want to send them the source code and let them download the arduino IDE.

We would like to send a firmware file, and an .exe file like a firmware upgrader, as most companies do. How would I start to go about this?

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Send them avrdude (including the config file) and the hex file. Look at the commands the IDE runs to see the right command format. You can then put that into a batch file if you like.

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