The separation of Canada in and of itself would not necessarily have any economic impact. It would be the nature of the separation that would cause such an impact. If the separation is totally amicable, there would likely be little to no impact.
On the other hand, if emotions run high and it pushes the country to the brink of civil war, then of course we'd quickly become a second-rate power over night.
Those are the two ends of the spectrum, and of course any separation could fall anywhere in between, with the economic impact being directly proportional to the friendly intentions on both sides at separation.
In the end, it's not separation itself that would would be to blame for any woes caused, but rather hate on either side for the other.
Having said that though, of course how we treat legal treaty obligations would likely play a significant role in how friendly relations are between First Nations too, and so any kind of animosity interfering with any possible friendly relations will certainly tear the country down more than any the administrative restructuring itself would, which technically is all separation would be at the political level at least.
Or to put it simply, economic health, though influenced by the top, is mostly determined by the grassroots.
Or to take another example, Harper's attitude demonstrated in his berating of the 'separatists' las year over the proposed coalition (which was not even to include the bloc anyway) will prove much more harmful to a post-separation economy than the separation itself, not to mention that such an attitude actually feeds sovereigntist sentiments as it denigrates the genuine democratic wishes of the people.