Yes, the debate over this video ended long ago, but I wanted to say something about it anyway.
From the video: "Is it your mesorah to pick only the most fantastical, irrational sources from the vastness of Jewish tradition and call anything else kefirah?"
I do think there is a tendency in the charedi world to see things this way. And the logic behind this approach is easy to understand.
In the last couple hundred years, Western civilization has accomplished a great deal by use of reason. At the same time, one cannot help noticing, religion has retreated in many different realms. Understandably, one can see this as a zero-sum game. Many charedim believe they are choosing religion at the inevitable expense of reason. Thus, all other things being equal, they tend to prefer the irrational and anti-humanistic over the rational and humanistic. They feel that the further an idea is from rationality, the further it is likely to be from rational atheism.
It is sometimes hard to determine what the Torah desires from you – particularly, which of the diverse and occasionally mutually exclusive approaches in the sources you should follow. When there is no other way of deciding between the sources, an understandable first step is to eliminate those which are associated – even if you can't fully clarify how – with atheism.