User bigfun is selling Atmega168 with the arduino bootloader. So it is possible. Check this thread:http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1159499314
can I then just write programs using the Arduino IDE and then upload the compiled .hex file without issues?
Yes, you can use Arduino sketches without the bootloader.http://www.arduino.cc/playground/Learning/AtmegaStandalone
"If you have an external programmer you can burn sketches to the Arduino board without using the bootloader. This allows you to use the full program space (flash) of the chip on the Arduino board. It also avoid the bootloader delay when you power or reset your board."http://www.arduino.cc/en/Hacking/Programmer