Story seems to be changing a bit
http://news.bbc.co.uk/2/hi/europe/5403976.stm
The hijackers were reported to have been protesting against the Pope's planned visit to Turkey in November.
However, confirming the surrender, Brindisi Police Chief Salvatore De Paolis told Reuters that the two men wanted political asylum.
...
However, Turkish television later said one of the hijackers had converted to Christianity and was a conscientious objector, Reuters reports.
It said he had sent a letter to the Pope in late August, asking for his help to avoid compulsory military service in Turkey. It quoted the letter as reading: "I am a Christian and I do not want to serve in a Muslim army."