It seems that Nunn (who is undoubtedly a stronger player than Chernev was) is correct in his criticisms of certain instances of analysis in Chernev's book, and also correct in pointing out that Chernev is sometimes too quick to dogmatically conclude an overarching general principle that doesn't properly allow for exceptions. But I don't believe this should cause you to read Chernev's book with caution (at least no more caution or skepticism than one should have when reading anything), and certainly not with paranoia.
The criticisms Nunn directs Chernev's way in Grandmaster Chess Move by Move are worthwhile things to hear for a player who is at an appropriate level to be reading Nunn's book, but the intended audience for that book is quite a bit more advanced than is Chernev's. The fact that Chernev makes certain oversimplifications (and yes, out-and-out mistakes in some places) is a good thing to be discovered at some point in a player's chess development, but this doesn't necessarily mean that Chernev's book, warts and all, cannot be (very!) useful to a beginner. [Consider: an absolute beginner reading Nunn's criticisms of Chernev that you cited wouldn't be able to appreciate the points being made at all: they would sail right over his or her head.]
The saying "One has to know the rules to break them" is applicable here. If you were to try and take every word in Chernev's book as gospel for the rest of your chess career, you would indeed be leading yourself astray. The same would be true if you tried to dogmatically follow, say, "knights should be developed before bishops" or similar overly general advice which is routinely thrown at novices. That doesn't mean that that kind of advice doesn't serve a useful purpose by giving newcomers to the game some first, rough guidelines to start learning from. I think the same can be said for Chernev's work; after all, it's not for nothing that this instructional book from 1957 is still topical today.