Come on, you lack imagination. Do you really not see that a simple change of units would solve the pb? It is a mere convention change, not even a technical change! Call 0.001 bitcoin 1 millibitcoin, or 1 mBTC, or 1 "new bitcoin". Done! They do this all the time in countries with inflation/deflation.

http://en.wikipedia.org/wiki/French_franc#New_franc