I've been doing it for 35 years - bearing accountant's advice that my salary had to be justifiable, and the CRA never gave us any grief about it. One difference over the years has been that there are now a lot more (highly priced) seminars on how to decrease taxes through various means on the greyer shade than we or our accountant (and probably you) would be comfortable with. On the CBC site there were some suggested tweaks.  One of them was that businesses had to have a certain number of employees threshold, which makes sense.  The problem isn't so much actual small businesses who contribute to the economy but with individuals who incorporate simply to avoid paying taxes. 
The messaging on this was very bad.  Whoever thought it would be a good idea to scapegoat doctors, who do have offices, staff, expenses, like any small business, should be sentenced to a week in the hospital.