Salman Abedi was 19 when he boarded the HMS Enterprise in Tripoli in August 2014 with his younger brother Hashem and more than 100 other British citizens.
It is understood Abedi's name was on a list of stranded citizens handed to the crew in charge of the evacuation.
The vessel took them to Malta where they caught a flight back to the UK.
In May last year, he killed 22 people including seven children at an Ariana Grande concert with a homemade suicide vest.
Dr Hilton, who blogs through the Archbishop Cramner website told Premier it's a sad and tragic situation, but people should not use this as grounds to categorise all refugees.
"What we can't do from this is extrapolate how we should treat all of those seeking any kind of asylum. We must not forget he was a British citizen, we had an obligation toward him and his family," he said.
"It wasn't a case of no we can't take you, stay in Libya - we were obliged to do so.
Dr Hilton added that the Bible gives the perfect example of how asylum seekers are supposed to be treated.
"The parable of the Good Samaritan is unequivocal in its view and advice to us on this," he said.
"We shouldn't discriminate against people on the grounds of ethnicity, or religion, or social status. We should seek to do good, to be passionate, to be merciful."
A Government spokesman said Abedi was being monitored by security services when he travelled to Libya, but his case was closed a month before his rescue.
The Anderson review into the Manchester attack found that the decision to close Abedi's case as a "subject of interest" was sound, based on the information available to security services at the time.
A Government source told the Daily Mail: "For this man to commit such an atrocity on UK soil after we rescued him from Libya was an act of utter betrayal."
Hashem Abedi is held in jail in Libya by a militia group, but the British Government has requested his extradition to face trial for his involvement in the attack.
The request has so far been refused.
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