Is there a way to make it run the interestingness script from the current directory and modify the original file? That is necessary for me to put the compilation step back.
You'd have to hack on C-Reduce to make this happen. I don't really recommend this. If you do it, be sure to turn off parallel execution (multicore reduction is the reason C-Reduce insists on running things from fresh directories).
Although I don't know your exact situation, it seems highly likely to me that you can find a way to compile your file in the temporary directory created by C-Reduce.
John