Well, the mcc18 compiler does not have a native Linux port, but it does run under wine flawlessly. Our team uses linux exclusively for FIRST programming.
For loading the actual program, you have several native options:
- rigel (command-line, supports all features of IFI_Loader including master firmware; open source. yes, this is a shameless plug for my own program

).
http://lights2dx.net/source/other/rigel-1.0-rc1.tar.bz2
- jifi (command-line and GUI I believe, and is Java based. Not open source as far as I know).
http://shtylman.com/frc/
- ifi-pictools (does basic read-write, open source) not sure of the link.
Any of these will work with regular RS-232 and USB RS-232 serial ports.