Published Tuesday, 11 December 2012
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The case saw 12 men acquitted in February of a range of terrorist offences, nine of them for the murder of UDA leader Tommy English in Belfast in 2000.
The former high profile defence lawyer said that he made the changes after he received "a very detailed judgement" from Mr Justice Gillen assessing the evidence and providing analysis.
"And I have been able to analyse that and prepare a formula under which the evidence of witnesses of this nature can be tested," Mr McGrory added.
"I have had meetings with senior police about this and certainly, I have had a number of meetings with my own senior prosecutors.
"So I think we are perhaps in a better place now to analyse and assess this type of evidence than maybe when the Prosecution Service was when that original decision was made."
The judge was very critical of key state evidence provided by brothers and self-confessed UVF members Ian and Robert Stewart, who had agreed to testify against the accused men as so-called assisting offenders in return for a lighter sentence.
Mr McGrory was not in the post at the time the decision was made to take the prosecutions - and told UTV that he would not comment on that aspect.
Future cases involving this type of evidence could be in the pipeline, with alleged senior loyalist and murder accused Gary Haggarty, 40, from north Belfast, having also turned state's witness.
Mr McGrory continued:"I don't like to measure prosecutions in terms of degrees of confidence of success. The test that we apply is whether or not on the evidence, there's a reasonable prospect of a conviction.
"If we set the balance higher than that we're accused of being risk averse and only take cases which we know we can win so there has to be some give and take in the process."
The Supergrass trial was more widely criticised over its cost after it emerged that millions of pounds from the public purse was spent on it.
However, the director said that he could not let future decisions be influenced by costs, before highlighting that the majority of the bill for the case was spent on defence lawyers.
Mr McGrory is calling for a thorough review of how legal aid is paid to defence lawyers, claiming they have access to an apparent "bottomless pit" of public funds.
He believes it is not right that around double that of the PPS's annual budget of £35million is being distributed to defence solicitors and barristers representing legal aid clients.
One way of bringing spending on all sides into line could be the creation of a public defenders' office, he explained.
The introduction of a regulatory measure over defence advocates was needed, with Mr McGrory claiming they were operating "a free market on the public purse".
"I think there needs to be a root-and-branch examination of the criminal justice system to have a look at just why the defence costs appear to be a bottomless pit," he said.
The head of the PPS acknowledged recent measures introduced by Stormont Justice Minister David Ford to reduce the fees paid to defence teams in criminal cases - but said more substantive reform was needed.
"In a sense I am poacher turned gamekeeper but I know it from both sides, and one of things that struck me coming into the prosecution service is how under-resourced it is compared to the defence," he said.
"I have to work at not getting annoyed when people say 'you took this case and it cost a fortune' - with the greatest of respect, the vast bulk of money that was spent on the case came from defending it."