Yes, unless Ben Stein didn’t simply neglect to enunciate a qualifier (such as the one that I’ve inserted in the following quotation) in which he actually believes, then he may, as Glenn Reynolds puts it, have “completely lost it”:

When we just saw that man, I think it was Mr. Myers, talking about how great scientists were, I was thinking to myself the last time any of my relatives saw scientists telling them what to do they were telling them to go to the showers to get gassed … that was horrifying beyond words, and that’s where science — in my opinion, this is just an opinion — that’s where science [as an ideological locus of meaning and moral guidance] leads you.

The added phrase would certainly be a legitimate response to biologist P.Z. Myers’s explanation, in the clip that Stein was referencing, that it was scientific learning that led him away from religious faith, and his hope that science would become the “main course” to the religious “side dish.” A more accurate culinary metaphor, from my point of view, would present religion as the set of beliefs and understanding of the world that sets the whys and hows of eating, while science helps one determine what to ingest toward those ends.
Automatically hearing or not hearing such important intellectual foundations as that which Stein conspicuously omitted lays, I believe, the central barrier of this particular dispute. Consider Reynolds:

The Holocaust was not a scientific endeavor, but had its roots in the Nazis’ unscientific loathing of the Jews. The Nazis did try to dress up that loathing in scientific dress, but that was a propaganda move, not science. (Indeed, Nazi science, for the most part, was dreadful science, made up by people to suit their preexisting beliefs without actual resort to the scientific method.)

And (via him), Ed Morrissey:

Science does not lead to Dachau; ideology perverting science led to Dachau. The Holocaust occurred when raving anti-Semites and materialists latched onto scientific theory as a philosophy, making it into a rationalization for what they would have done regardless.

Reynolds elides the reality that the trappings of science make for effective propaganda, and Morrissey is too quick to treat science as a passive body of knowledge, as opposed to a mode of thought that can have an effect on the thinker. It is an error to suppose that science can define, explain, and qualify everything that is important in life — or even just important in intellectual inquiry — but the implications, when once that error has been made, do lend themselves to dangerous conclusions. The lack of an anchor against tides of explicability and direction facilitates rationalization of ghastly experimentation and application.
Something similar can be said in general of religion, of course, and science is among the anchors to prevent that particular drift. The danger of current polemics is that the distance between us will grow as we pick and choose which types of ballast we may permissibly jettison. And we do well to grant a benefit of the doubt to those of the other side when — in one-take broadcast conversation — they appear to have left some disclaimers unsaid.