Bitcoin it is a currency anti inflation, and it is best to reflect that fact.
That's why I believe it is important to make that change as soon as possible. Currently, there's only around 60.000 people trading with Bitcoin at Mt.Gox. That's almost nothing compared to what it will very likely be in 3 months, 6 months, 12 months. So, while such a change already is kind of painful, the longer we wait, the more painful it become.
Mathematically, it may not make a difference - but what matters is the difference in perception: No one wants to work with a currency where you have to do transactions like 0.0001 BTC sent over. That simply doesn't work. However, sending around 100 uBTC seems reasonable. The way I see it, Bitcoin is especially interesting for microtransactions - and for that specific use case, the current way the decimal is handled is just wrong.
Of course, that kind of change must be communicated wisely ...