An American intelligence analyst should be ardently pro-American.
If he's ardently pro-any-country-other-than-America, he's a serious security risk. He shouldn't have a clearance.
Being pro-Israel doesn't mean the guy wasn't pro-America. Notice he wanted to establish governments in the Arab world friendly to America. But, as you say, he is a threat if he doesn't follow the rules of his position, and should be punished if he broke any of them.
The reason I said his religion was interesting was because there were rumors going around before hand that it was a Jew doing this, and people were talking about the "dual-loyality" of the Jews.
You Arrogant Bustard! You can't tell anything from a press report, particularly one leaked by un-named sources close the the investigation. So let us wait and see what happens before we run our blood pressure up over shoulds and oughts. ;-)