I put it this way in "Lapsing Into a Comma":
This doesn't mean we need to reproduce every um, every er, every cough; it doesn't mean a reporter's transcription errors can't be corrected; and it certainly doesn't mean that stories should attempt to re-create dialect (plenty of literate people pronounce should have as "should of"). But it does mean that a reader should be able to watch a TV interview and read the same interview in the newspaper and not notice discrepancies in word choice.
The pronunciation issue is just one of the complexities within the bigger question. What about quotes from written material? If the Senate subcommittee's report refers to "the President," are we at liberty to make that "the president"? It's a slightly closer call than changing a spoken "ain't" to "isn't," but I think the answer is still no. The attribution "the panel wrote" should introduce what the panel actually wrote.
Now then: What about written material of a less-formal nature? More and more these days, instead of making a phone call, a reporter will ask a source a question by e-mail. If Deep Throat '05 writes, "dood that documnet, thats the smokin gun!!!!!," what do you quote your source as saying?
My answer may surprise you:
"That document, that's the smoking gun," the source said.
E-mail is the medium, not the message, and informality in spelling, capitalization and punctuation in e-mailed answers is akin to pronunciation in spoken answers. All this, for me, hinges on the verb "said." Whether you must disclose "said in an e-mail interview" is an issue for your publication's masters (Do you say "said in a telephone interview"?), but once you frame your quote in terms of "said" rather than "wrote," you become a literate transcriber rather than a photocopier. More controversially, perhaps, I would extend this liberty even to "said in a news release." If Acme announces news about "WILE E. COYOTE" in a release, go ahead and make it "Wile E. Coyote," as long as you're saying "the spokesman said" or "the company said" rather than "the news release said."
That news-release guideline is an exception to my general advice, which is to treat documents as sacred when they are intended to be read by an audience other than the reporter. When you're quoting an e-mail to yourself, you're quoting the writer of the e-mail, you should use the verb "said," and you should follow your publication's style; when you're quoting an e-mail from Enron felon No. 1 to Enron felon No. 2, you're quoting the e-mail, you should use the verb "wrote," and you shouldn't change things.