There isn't a way to write an arduino program in java, as the arduino is too slow and doesn't have enough memory to efficiently run a JVM. However, C is simpler than java (it isn't object oriented), and any program that is written in C will compile in a C++ compiler, which is an FRC supported language.
If you are interested in learning C for arduino, check out the arduino playground for inspiration.
If you do not wish to learn a lot about C, you could write a simple C program for the arduino, that transmits all of the inputs that you are interested in over serial to the cRIO, and receives all your outputs from the cRIO (like the LED light information). Remember, you need to use a level converter for serial communication between the two, as the cRIO uses RS-232, and the arduino uses TTL.
If you are not interested in reading inputs like sensors, and only having the arduino use outputs (like the LED lights), you could use
this library from the arduino playground.