If you download the library you will see that we offer it in Java, CPP, and C. These are all suitable for running in the linux environment. You should be able to use GCC (C/C++) to compile a static or dynamic library that utilizes the FIT messages and types as needed. Or you can get the Java JDK from Oracle to compile the java code (or link against the fit.jar provided).
The CSV conversion is for convenience of reading files only. If you open the CSV file in a programming editor (like Notepad++ you will see it literally just separates every value by a comma).