The Arduino system is really just an editor (for ex. vim), a set of libraries (download from the website), a compiler (avr-gcc), and a programmer (avrdude). If you're already experienced in how to work with commandline C/C++ development tools, you should be fine. Search around here for the CMake version, which should be compatible, with some slight modification, for your purposes. Alternatively, you can write your own makefile.
So yes, you can develop on Arduino without java. Look into AVR development in Linux - the only thing you'll have to change is uploading (avrdude -carduino) and linking in the Arduino libraries (compiler + link).