I have never used NitDroid on my n900 but I imagine it would be possible to read and write to other sectors of the eMMC.

I'll leave it to the guys who have actually used NitDroid to give you a definitive answer on that one.

I'll keep trying to figure out a way for you to rescue your install (You need to bypass that messed up hildon-desktop somehow) and if I think of something I'll be sure to post about it.

Sorry I wasn't able to help you resolve your problem.