With ongoing media reports, it has become increasingly clear that the main reason for the imprisonment of Ben Zygier, "Prisoner X", in Israel, and the method of his imprisonment, were primarily meant to have him disappear and save face for the Israeli government and secret services for a major failure.
The reports make it clear that Zygier was unfit for the job into which he was recruited. He started telling friends right away that he was working for the secret services. Later, his betrayal, if any, was also most likely related to talking - probably to the Australian investigators. Finally, his imprisonment as "Prisoner X" was meant to deprive him of any further contact with the outside world, including his wardens.
The same is true of course of many or most of those, who remain detained in Guantanamo Bay, Cuba. From what has been published, it is clear that many of the detainees were captured, imprisoned, and tortured as part of mistaken identities, of account settling in their countries of origin, etc. At this point, some of the detainees are even held for long time periods, after the US government already decided on their release. It appears that today, the main reason to hold on most of the Guantanamo detainees is simply to hide the failure of US security services in handling the entire affair. If the prisoners could be held until they die, that could have been the best outcome. Otherwise - hold them as long as possible, to prevent them from telling their true stories.
There is nothing spectacularly surprising about such state of affairs. That is what governments doe - when they are permitted.
 Ben Zygier was no traitor, he was betrayed
 Marking 10 years since Guantanamo’s opening, the ACLU releases report on Guantanamo detainees