Imam Samudra and brothers Amrozi and Mukhlas were shot by separate firing squads in November 2008.
Former Liberal Prime Minister John Howard said the executions were "appropriate" and any reduced sentence would have offended the families of the 88 Australians killed in the bombings.
His Labor successor, Kevin Rudd, said the three men were "cowards and murderers pure and simple" and that they "deserve the justice that will be delivered to them".
McRae says that Australia's stand on the death penalty has been compromised, undermining its chances of influencing other Southeast Asian countries, and the Government must avoid further equivocation on capital punishment.
"No advocacy will be effective if Australia is not a principled and consistent opponent of the death penalty."
The only Southeast Asian countries to have abolished the death penalty are the Philippines, Cambodia and Timor-Leste, and in Indonesia Chan and Sukumaran are among 114 prisoners on death row.
Both Chan and Sukumaran have exhausted their final avenues of judicial appeal, and can now be saved only by the granting of clemency by President Yudhoyono.
But only one prisoner has gained clemency since 1990, while 22 executions have been carried out in the past 14 years.
Last year Yudhoyono said he rejected almost all requests for clemency in capital cases from foreign nations: "If our citizens receive the death penalty for very serious crimes and problems, why should we then grant clemency to other countries' citizens?"
Indonesian courts have also recently upheld the death penalty for narcotics crimes, rejected claims that execution by firing squad violates constitutional protections against torture, and a court is at present hearing a challenge against death sentences for robbery causing death.
But McRae says there are factors that Australia could use to influence Jakarta - including Indonesian revulsion at executions of Indonesians abroad - and that immediate benefits could flow to Chan and Sukumaran.
Wider gains could include greater protection for other Australian travellers, possible momentum for more Southeast Asian countries to scrap capital punishment, strengthening of Australia's international credibility, and a lowering of potential diplomatic flashpoints.
But it would mean working to save terrorists' lives, McRae says.
"A key step would be to signal its opposition to any and all executions in Indonesia, to re-establish Australia's position of consistent and principled opposition to the death penalty."