I visited Israel in August 2012 after having been in Iran in January that year.
The first immigration person I got was not happy about the Iranian visa and stamp, and seemed incredulous that I would ever want to go there. He actually said "There is nothing worth seeing in Iran". He asked me a lot of pointed questions, and was slightly aggressive, then sent me to wait for secondary processing.
After a 30+ minute wait I was then shepherded into an office and grilled by a female IDF agent. They ask a lot of questions they don't even know the answers to, such as where you went to school and where your grandparents were born - the point is they are looking for 'tells', not that they are checking the answers themselves.
If your story checks out, and they don't think you are an activist (or terrorist!) it is highly likely that they will let you into the country. I was there for the wedding of a close friend, and they ended up calling him to verify that, and once they'd spoken that seemed to clinch it and they let me in.
The grilling was pretty full-on though - I was really freaking out, and tried to make the situation better with humor but they are too disciplined and have had their sense of humor trained out of them. At one point the girl (she was really only a girl, early 20s maybe) pointed down at my hands, which were shaking like I had Parkinsons and said, with deadpan face - "You are shaking. Why are you shaking? Are you nervous?"
To which I responded: "I guess I'm just intimidated by Israeli women". She didn't crack even a glimmer of a smile.