I am a big fan of the serial comma, and I think that it provides necessary precision in instances where a lack of punctuation might lead to misinterpretation of which entries near the end of the series go with which. But style guides that typically do not use the serial comma make exceptions to handle such instances. Thus, for example, The Associated Press Stylebook (2002) says:
IN A SERIES: Use commas to separate elements in a series, but do not put a comma before the conjunction in a simple series: The flag is red, white and blue. Tom, Dick or Harry.
Put a comma before the concluding conjunction in a series, however, if an integral element of the series requires a conjunction: I had orange juice, toast, and ham and eggs for breakfast.
Use a comma also before the concluding conjunction in a complex series of phrases: The main points to consider are whether the athletes are skillful enough to compete, whether they have the stamina to endure the training, and whether they have the proper mental attitude.
As this handling of commas in series indicates, the circumstances under which the AP style guidelines advise a writer to omit the serial comma do not raise issues of readability or understandability at all. Rather, they fall into a narrow area where inclusion or omission of the comma is simply a matter of style.
Consequently, opposing that approach in a situation like yours, where serial-comma-less quoted material appears in the midst of text that follows The Chicago Manual of Style in preferring the serial comma, is not a matter of correcting misleading or ambiguous punctuation decisions, but of imposing one publisher's house style on material from elsewhere that (presumably consistently) followed another style. In my opinion, MetaEd is correct in saying that such alterations exceed Chicago's mandate to correct obvious typographic errors.