The purpose of federally funded scientific research is not and cannot be to support the policy objectives of the currently sitting government.
So a real answer to the putative problem might be to have an arms length communications office review communication for accuracy, but one that does not directly answer to the PMs office or federal PR. What Harper did was far more draconian than that. At the same time he initiated other damaging actions to federal science, so you can hardly fault people for not trusting the motives. He could have solved this easily by making things arms length, and chose not to, as well as choosing to be very opaque about the whole process. If for no other reason than that, his government deserves all the criticism it has had on this account.