With a majority government, that approval is guaranteed because the government controls the vote. Given the strong tendency in Canada to toe the party line, it would not be a problem.
In a minority government, it would spark a debate that would have to yield a general consent.
The Standing Order could, however, be drafted in such a way that only the Prime Minister, for instance, would have the power to put the question to the House. It could be structured so that the Prime Minister would retain the right to take the prorogation initiative, instead of letting everyone move a vote on a resolution, a motion on prorogation—somewhat similar to the idea that only the government can introduce a money bill.
That would respect the principle of government initiative while requiring the consent of the elected members.