Let's start with the issue of the mandatory minimum sentences. It seems to me that even though the government is admitting they made a mistake, or carried over a mistake from the previous bill without correcting it, and are now saying that the mandatory minimum sentence of nine months only applies to people who have six marijuana plants, organized crime, grow-ops with six marijuana plants, the difficulty is that it clearly ends up with a disproportionate sentence. No matter how we look at that, if you look at the range of sentences that are available in Canada, very few people are going to say that my hypothetical student with six plants or one plant--it doesn't really matter--is now deserving of nine months. So what will happen or can happen is that deals can be made.
Another way to deal with the problem of sentencing would be to have reasonable sentences without mandatory minimums, and some form of guidelines. Canada rejected the idea of sentencing guidelines more than 25 years ago, but that doesn't mean that the proposal for guidelines that was made in the 1980s is the only one.
Other jurisdictions have looked to ways in which they can structure sentences in a way that makes sentences more coherent and more fair when you look at sentences across the board, so that they have a sentencing system based on proportionality. Mandatory minimum penalties almost certainly violate or force the violation of the principle of proportionality. As you implied by your question, they also give over the power to sentence to the prosecutor, so that the prosecutor can in effect extort agreements to plead guilty by saying that certain elements won't be proved--in this case, for example, that it's a rented apartment.