Keesio, I think if the purpose is to address marriage fraud, then this rule should only be applied if the marriage was fraudulent.
In the US, there is a conditional PR rule. After two years together, they re-evaluate whether the marriage was genuine. At this point, if you've been living together, you prove that. If you haven't been living together because of a breakdown of the relationship, they will look at whether the marriage was genuine. Obviously, they look more closely at these cases, but if you show good evidence that the marriage was genuine when you came to the US, and then you separated, then that's totally legal.
I don't find it acceptable that anybody should be locked into a relationship in order to continue their life in Canada, once they've already established themselves here (a job, children perhaps, etc.) I know there are exceptions for battered wives, but honestly I don't think that if you leave your spouse for reasons besides violence, it means you were necessarily dishonest when you came to Canada. It would be preferable if Canada simply took a fresh look at these relationships, but still not penalize anybody who was honest starting out.