Yesterday I thought that the Governor General should not grant a prorogation of parliament, but today, after reading and listening to various opinions, I agree that she made the right decision.
The Prime Minister had the technical confidence of the House because the motion accepting the speech from the throne passed and it is not her place to question that confidence.
The correct solution to this problem, as I heard suggested, is to amend Parliamentary procedure to require a confidence motion on prorogation before the Prime Minister is allowed to go to the Governor General. This would prevent the Prime Minister from abusing his power by proroguing parliament before a confidence vote.