Trojans don't modify kernel files. Also, a trojan only affects Windows OS if it is to get infected and should stick to Windows only. From my experience I have tested Mac, Windows, Backtrack, UNIX everything and I have never heard that any OS installed next to Mac affected its good functionality.
Once you install Windows using Bootcamp the system or any other threat can't access those files in write mode, can't even modify them, only read and reading is also complicated even for a trojan on Windows.