When the history of the SA government’s handling of the Covid-19 crisis is written, one of the things that will deserve special mention and provide a lesson for future administrations will be its knack for shooting itself in the foot.

President Cyril Ramaphosa and health minister Zweli Mkhize have won praise for their style of leadership and communication, which has allowed them to take people along even when decisions look difficult and unpalatable.

And then they hand things over to their lieutenants and see it all fall apart.

Ramaphosa’s May 13 address to the nation was another well-received speech in which he showed that he had the humility to own up to mistakes. That was soon followed by decisive action in undoing Ebrahim Patel’s ludicrous ban on e-commerce. There was even a promise that the government would revisit its policy of allowing exercise during a prescribed three-hour period.

It seemed to be working for a while. With Patel kept out of the headlines, the mood seemed to be changing for the better. And then, as always, the president stayed quiet for too long.

In that vacuum, space was created for more ludicrous statements from ministers that undermine trust and the spirit of co-operation, the latest being the utterance at the weekend by the police minister suggesting that he had unilaterally criminalised smoking.

Bheki Cele’s statement has given the police, who have already been implicated in human rights abuses together with members of the army, the right to harass smokers and ask them for proof of purchases. Its senseless in more ways than one — those who bought cigarettes before March 27 are unlikely to be carrying slips, while those who are making a killing in the booming illicit trade that has been given new life by the government’s ban on legal cigarettes are hardly going to be handing out proof of sales.

And now there’s a completely unnecessary controversy over a scientist’s right to free speech. Mkhize’s initial response to the comments attributed to Glenda Gray, the head of the Medical Research Council (MRC) and member of the committee advising the minister on the health aspects of the Covid-19 response, was exemplary.

Gray made headlines with hard-hitting comments to News24 on the government’s approach to the lockdown. Some of the comments have been “clarified”, partly in response to a thorough and precise rebuttal by Mkhize.

The minister earned full marks with a measured response that, while making his annoyance clear, was respectful and stuck to the facts. He went to great pains to explain that having an adviser doesn’t equate to delegating decision-making and the responsibility that comes with it. He acknowledged that the government, in tackling an unprecedented crisis, would have missteps and rightly mentioned that “divergent views by scientists are healthy and welcome”.

Having got the moral high ground, the government should have left it there. The intervention by the department’s acting director-general Anban Pillay, who instructed Johnny Mahlangu, chair of the MRC, to investigate Gray’s conduct, was unwise and unacceptable in a democracy.

The government is within its rights to make its displeasure known, but Pillay’s mere mention of the MRC’s relationship with the department cannot be seen as anything but a veiled threat. He went further, making allegations about Gray’s conduct on “other matters” that he didn’t specify.

It’s one thing for the ANC’s national executive committee to try to silence finance minister Tito Mboweni after he voiced dissenting opinions on the ban on tobacco and alcohol sales. Academics and scientists are not ANC or government cadres and therefore cannot be subjected to the same discipline. It’s not only their right to voice opinions that challenge the government, but their duty.

By all means, criticise and challenge Gray’s views — and the number of clarifications after the initial interview indicate there were inaccuracies that needed to be corrected — but in a constitutional democracy that values academic freedom, the government has no right to bully her into silence.