When it comes to what he describes as hard-news coverage, they should report what was said and leave it at that. There are plenty of ways for people to discern what's true and what's bogus. Editorial departments can and should point out when somebody's full of shit. Also, the article can link to Factcheck.org. Truth is, most people don't just read the Times and assume it's factually correct, anyway. Nowadays, people get their news from a variety of sources and have a much easier time discerning fact from fiction.
Also, this doesn't apply to interviews or press conferences. I'd like to see more of those guys being hardassed about obvious bullshit. Said Times reporter should be willing to press the fact that Thomas is lying when he's there to reply, but when he reports it, he should stick to what was said.
FOX's "we report, you decide" is exactly how it should be done. It's just a shame that they don't actually believe it.