I heard before that Israeli security can be scary if they sense you went to either Palestinian areas or some of their flags get triggered. But no excuse for them to do what they do.
I hope you raising this issue help you get your laptop back.
I personally worry that they might take my laptop from me and install some spyware, so I try not to carry one, or if I do, travel with Chromebook. Whenever I can get away without carrying laptop, it is huge relief to just breeze through customs. Essentially excuses they have to talk to you are diminished and potential for some unpleasant interaction are greatly reduced.
I carry Kindle and if I have to Chromebook, life is much simpler. Friends borrow me their laptops if I have to do some work.
Again, sorry for what is happening to you, I can't even imagine how horrible you are feeling, hope for quick and positive resolution.