I have a feeling, though, we dont have all the story here, particularly given the fact that he approached the press. As an ex Ranger (?), there are other units in which he could serve. The article ignores the fact that he is an expert on Middle Eastern affairs, and an advisor to several Israeli think tanks (odd, since he has written for the JP). Given the nature of some of his writings (see links), and particularly the fact that he is in a linguistics unit, his background would appear to be a real asset in MI.
A natural born US citizen for his first 17 years, the service in the IDF would have been mandatory when his family relocated. It wasnt his option. Interestingly he returned here after his 3 years of service. The loyalty issue, based on his youthful IDF service and dual-citizenship is nonsense. Most 17 year olds will relocate with their family.
I suspect there were reasons for his clearance loss that we dont know. It could be as simple as the time spent training with his unit, since he seems to have active in other pursuits the last 6-7 years.