In the context of language-arts education, a certain prescriptivism is unavoidable. There is a written standard, like it or not, and there are social consequences to violating the standard in certain contexts.
So I agree that students should be taught 'the code'. But (and here's the tricky part), how do you do that when most teachers have a very scanty knowledge of the underlying principles of language?
There are any number of problems with the way language fundamentals, by which I mean the whole bundle of skills that somewhat inaccurately goes under the label of grammar, are taught.
Many teachers have little or no training in the sort of grammar that will help them actually understand (and correct when necessary) the lessons they are expected to teach. The textbooks in use in K-12 classrooms are little help. They contain numerous misleading or outright false statements about English grammar. They are often poorly edited, with flawed exercises and errors in the answer keys.
In that context, it's only natural that teachers take refuge in traditional severity. It's their way of establishing their authority when in fact their training has not prepared them well to have any real mastery over the content.
For this, by the way, I don't blame the teachers. The NCTE has long deprecated formal grammar instruction, and in most teacher preparation programs will not remedy that deficit. At best, teachers in training get one, or if they're lucky two, semesters of linguistics/grammar, and depending on the attitudes of the professors running those courses, they may come out with more exposure to technical generative grammar than to something that will be of direct use in the classroom.
The correspondent that Thomason quotes seems to have a very sensible approach to the issue, but it's also worth noting how rare such people are in the classroom. You can tell this by the reaction of her students:
I've had more than one student come up to me after an ACT class and say, "You're the first English teacher I've had who didn't tell me my mother spoke like an uneducated hick," or "This is the first time anyone's explained why standard usage is important."
In other words, most teachers take a judgmental attitude towards usage, without giving any good reason to justify it. Is it any wonder that linguists complain?
How do we fix the problem? It's a tough one, because there are many interlocking parts, and changing one depends on changing others.
One important thing we could do, though, is insist on accurate information in the textbooks. This is hard to do, of course, since textbook adoption is highly political, and there are strong financial motivations to stick with the status quo. But accurate textbooks would at least give new teachers, who are trying to master the material themselves (not having ever really learned it in school) a fighting chance to approach questions of prescriptivism with a sensible balance.
Another important shift would be to spend teachers efforts on what really matters for Standard English. Learning how to punctuate sentences so as to avoid both run-ons and fragments, for example, is not trivial. It actually requires a fairly full understanding of phrase and clause structure. This sort of information is important in a practical sense, and the prerequisites to understanding it wind up teaching students something very valuable about the way language works.
On the other hand, drilling students on the predicate nominative is a waste of all-too-scarce classroom time. Standard English is typically sold in terms of the gate-keeper threat: you won't get the job/promotion, etc. if you don't conform. It's debatable, however, whether or not most people actually notice many of the minutiae of usage books (data as a plural noun, hopefully outlawed as a sentence modifier, etc.) unless they are reading as editors or English teachers (i.e., reading in search of error). For an illuminating illustration of the effect that error sensitivity has on our perception, see this classic article by Joseph Williams.
If you are a teacher who needs to cover grammatical topics, I sympathize with your plight. Go ahead and teach Standard English, but please, be sensible about it.