Ugh - I suppose it's possible but I wouldn't want to do it. Depending on where in Vancouver, you might have a heck of a commute to get from the ferry terminal to your workplace (and the same on the Nanaimo side). There are two ferries going from Nanaimo to Vancouver, one on the north and one on the south. One is longer than the other but even the shortest one is 1.5 hours on the boat...assuming it leaves on time. The walk-on fare is now up to about $15 one way although they may have commuter rates, I'm not sure. I hope you figure something out, because this would not be my ideal plan at all, although the housing prices in Vancouver are enough to turn anyone off. Maybe someone who does it will chime in here...
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