I'm glad to announce that I have finished my Import/Export N to N relationships tool for CRM 2011.
To use it all you have to do is to download solution, install it and try:
Comments and suggestions are welcomed.
UPD: In case you are getting error like 'Issues on line 1: Line has 1 instead of 2' the possible issue is in encoding of your source file. Save your CSV using Unicode encoding and repeat your attempt. I have already fixed the code to work with any encoding but unfortunately I'm too busy at the moment to fix and publish the whole solution again.