I read the articles, and it really is embarrassing. Alpher lays out a bundle of accusations and insults there and barely argues for his position. The most serious argument implied there is that there is no “empirical” proof—that is, the kind you can perform in a laboratory—for the existence of God, and therefore—notice the leap—belief in Him is stupidity.
There were a few response articles. I think only one of them touched on the point that we also believe in things that are not measurable, and that this is rational and not far-fetched. But it did not go into the arguments proving the existence of God. Menachem Ben also wrote something. He used a certain version of the cosmological argument, but the presentation was more like a synagogue sermon and lacked a careful logical structure. It was something written as if under inspiration. So he brings there a claim—it doesn’t seem to me that it proves anything—that God’s existence is proven from the language of the Hebrew Bible, which is divine. For example, the first verse would have been written “the firmament and the ground” if it had been written by a human being, instead of “the heavens and the earth.” A bit funny, no?
In the end, no serious response article appeared there, and that’s a little annoying. It’s annoying partly because it could strengthen the impression among some people that believers have no serious arguments backing up their faith. But it’s mostly annoying because Haaretz has an image—at least among the public that reads it—of being an educated, high-level newspaper, and in practice the material published on this topic was pathetic, demagogic, boring, and disappointing.
I haven’t had many chances to read Haaretz, so I don’t want to generalize and make claims about most of the material published there, but anyone who knows it better is welcome to point to additional cases of this kind.
And to Rabbi Michi: it really, really would have been appropriate for some article by you to be published there. Are you really so sure that if you send one they won’t publish it?
By the way, Abed L. Aziz also wrote something there. Most of it was teleological claims like religion brings murder, poverty, and so on—not worth reading. But he did make an interesting argument. After accusing Christianity and Islam of the historical murder campaigns they carried out (and Islam still does), he said: we Jews should not rejoice in our innocence. We were simply few, marginal, and weak throughout history, and therefore we did not have the ability to commit such atrocities. What do you think? If we really had been large and powerful, would crimes have been committed in the style and scope of our monotheistic cousins?

From my experience, the chance that it would be published is next to zero. There’s no point making the effort to write it only for them not to publish it in the end, and I don’t have the time.

That claim was already raised by the King of the Kuzars. I want to believe that we wouldn’t have done that, but who knows…

If Alpher sees as stupidity anything that can’t be measured in a lab, then is “belief” in morality also stupidity?

Itai, they’ll answer you that they have no belief in morality. Their claim is that it’s stupid to accept the existence of something for which we have no empirical evidence. But morality is not an existing entity, and obligation toward it is not a factual claim, so it is not subject to the demand for empiricism.
I agree with the morality claim, but it requires a more detailed justification. See the fourth notebook.

What difference does it make whether logic creates obligation or existence?
And by the way, even a laboratory test does not create a true law, as the late great Rabbi David Hume said, and if so then empirical testing also rests on logic, and consequently relying on empirical testing is stupidity. Of course, Alpher won’t accept that claim either, since it wasn’t tested in a laboratory…

That is already a different argument. In my books I expanded at length on my response regarding this issue: that even the empirical is based on the rational. But the argument that dealt with belief in factual claims is not connected to moral obligation.