Haven't you heard? Jews are not a religion and every "ethnic" Jew automatically gets Israeli citizenship.
Must be a new definition of "Jew" I hadn't heard before.
As far as citizenship is concerned even if an American Jew makes aliya (moves to Israel) they do not automatically become citizens. Many younger olim take tempoary resident status for three years to avoid being drafted during what is already a sometimes difficult transitional period for an oleh hadash (new immigrant). If they took citizenship immediately they'd be subject to IDF service 90 days after they arrived just like any other Israeli. Some choose to return to the States without ever taking citizenship.
My dual nationality derived from 1) being the child of an Israeli born overseas and 2) having then lived in Israel as a child. I'd assume my parents did whatever was necessary for me to be considered a citizen. We did move back to the States but my citizenship remained.
FWIW, I held a security clearance in the U.S. for some time. I had to state that I had citizenship in another country on the paperwork I filled out when I as subject to a "National Security Background Investigation". The issue of my having lived in Israel as a child and having family there most certainly was questioned. I answered all questions honestly and my clearance was granted. The clearance was subsequently revoked in 2001 due to changes the Bush admininstration put in place. The Clinton administration permitted clearances to people that the Bush administration later denied. I cannot honestly say if this was a general tightening up of security or if Israelis were particularly targeted, but with lack of factual information I'd assume that it was a general change in policy.
There is a general distrust of Israelis in the American security establishment in my experience. The Pollard affair definitely had something to do with that.
Are Jews descriminiated against in American security positions? In some situations that has been well documented. Sephardic Jews (Jews who fled Arab countries) have been denied Arabic translator positions for fear of offending Arab-American translators. Sephardim are native Arabic speakers who are generally very loyal Americans who have no love for the Arabs who drove them out of their homelands. Some Arab-American translators proved to be, well... not so loyal. In this one instance I feel DOD and the intelligence community did themselves a very real disservice in barring Jews from sensitive positions in a way that did not serve American security interests.
Is there a more general discrimination against American Jews? I didn't seen it when I lived in the States and worked for the government. Prior to the Bush administration there certainly was no discrimination against Israeli-born Americans either in some positions requiring clearance. It depended on the level of clearance required. Again, I know this from first hand experience. Having said all of that, I will NOT accuse the Bush administration of having any particular agenda against American Jews or Americans who immigrated from Israel until I see some evidence of it. One paragraph from a magazine is insufficient to make such an accusation. If the Bush administration does have such an agenda they are only hurting themselves.