The article said Dr Hamilton had warned about the unit before a mother took her own life in 2011 after she was allowed to leave the hospital. The mother mentioned in the story had been the Waggitts' daughter, Claire Donald, who threw herself off the Erskine Bridge.
They had been trying find out why their daughter had been let out of the Mother And Baby Unit (MBU) when she had twice tried to take her own life in the preceding months.
On hearing of the attempts to gag Dr Hamilton, Mr Waggitt said last night: "When we read in The Herald that a doctor we had never heard of had tried to warn about the MBU, only to suffer for her trouble, it made us think long and hard.
"The more so after the health board tried to gloss over everything in a letter to The Herald, which really shocked us. That is what made us go public about Claire's death. However, we are now left with this one recurring thought - if only they had listened to Dr Hamilton."
He said he and his son-in-law Graeme Donald now hoped the truth would be revealed in their impending civil action against NHS Lothian, but added that they should not have to go to these lengths.
Certainly, most thought that the position of whistle-blowers within the NHS was now secure and gagging clauses had been outlawed.
Last February, Robert Francis, QC, chairman of the public inquiry into failings at Stafford Hospital, in the Midlands, made clear a culture change was needed.
His inquiry found that years of abuse and neglect at the English hospital had led to the unnecessary deaths of hundreds of patients. He said NHS staff should face prosecution if they were not open and honest about mistakes, stressing the failings went right to the top of the health service.
A fortnight later Scottish Health Secretary Alex Neil wrote to all the country's health boards to reinforce the message. He said they should ensure they had a culture that actively encouraged staff to raise concerns.
"The culture should also ensure staff are not penalised or persecuted in any way for raising concerns in good faith, " he said.
In case there was any doubt, Mr Neil said: "I am writing today to take this one step further. NHS Scotland does not have any policies that would prevent, or would condone, the prevention of staff from raising concerns about safety and quality, not least because it would be illegal.
"I therefore wish to make it clear that I expect boards to ensure confidentiality clauses and non-derogatory statement clauses are not used to suppress the reporting of concerns about practice in the NHS in Scotland."
The Scottish Government also introduced a confidential alert line for NHS whistle-blowers , last April. Dr Hamilton phoned it, but it simply referred her back to the health board. So there is still concern.
Rab Wilson, the former psychiatric nurse who exposed errors surrounding the deaths of 20 patients in NHS Ayrshire and Arran, is not convinced by the confidential line.
He said: "From what I have heard, anyone who phones up usually finds they are referred back to their employer. It's a bit like Mrs Hen phoning up to complain her chicks are being eaten by foxes raiding the coop, and she gets referred on to Mr Fox."
He has now lodged a petition at the Scottish Parliament that seeks to further protect NHS whistle-blowers and ensure gagging orders are truly ended.
Some 697 compromise agreements, most with gagging orders, have been paid out to former NHS employees over the past five years, at an average cost of £29,000 per payout, or £20.2 million in total.