http://hex2bin.sourceforge.net/

once you do that go back into arduino and into option set output to verbose for compiling and the last few lines in the output window will tell you where the hex file is.. On my machine it is C:\Users\CARLXXXXX\AppData\Local\Temp\build6270018850889749836.tmp/Repetier.cpp.hex

I am not sure and it won't really hurt anything as it will just fail and you can go back to the stock version but I think you can just change the extension of .hex to .bin and it works. Honestly because of the way the Due is programmed it is near impossible to brick it. You simply short the jumper and use bossac with the original bin and your back to where you started.

Is there Repetier firmware in *.bin format for DaVinci 2.0 that I can flash with bossac.exe?

You can make it, when you compile a file in Arduino it creates a temporary file called very long string of numbers.bin. that would be the bin file you can use. Just rip from arduinos working directory.