(1) Keep the headlines and the body of the article distinct. At least, unless you know the inner workings of the news source in question. In many cases, the person who wrote the headline, at least in its final form, isn't the same person who wrote the article, so you shouldn't assume they are, even though together they form one finished article. In this case, the headline is fairly reserved, whereas the lede is not.
(2) Neither the headline nor the lede should be taken at face value unless adequately supported by the rest of the article. This is just common sense. You don't accept conclusions just on the basis of their being conclusions, do you? Of course not. The headline and the lede are, in different ways, conclusions of journalistic research. When we are faced with them, we should look to see what evidence is presented in support of them. In this case, the headline has some basis in the article. The headline says, "The fires of Hell are real and eternal Pope warns." The article quotes the Pope as saying, that hell "is real and eternal". This isn't full support for the headline as presented, since the article doesn't even have the Pope mentioning fire; and one could argue it is misleading, since it is ambiguous in meaning depending on whether we take 'fires of Hell' as a metaphorical expression or a literal expression. (Obviously, the expressions used to talk about something real may be either metaphorical or literal.) But ambiguity is just a natural hazard of headline-writing, so as long as we keep the danger in mind, it's not worth getting worked up about in any way. The lede is considerably more bold. It says, "Hell is a place where sinners really do burn in an everlasting fire, and not just a religious symbol designed to galvanise the faithful, the Pope has said." But it quotes nothing from the Pope that supports this claim, and on the other hand quotes Vatican officials as saying that the Pope was speaking "symbolically, rather than physically." The lede is poorly supported by the evidence presented.
(3) Compare the reporting with alternative and independent reporting. A lot of the articles floating around, particularly although not exclusively from smaller news sources, were derived directly from the Times article. However, the Guardian had a very different report, one in which the headline and lede are both well-supported by the article, and which paints a rather different picture. Despite placing less emphasis on it, it gives more of the "is real and eternal" quotation than the Times does. It then goes on to say:
The talk of fire and brimstone stopped there, as Pope Benedict failed to elaborate on what lay ahead for the sinner in the afterlife, adding only that "our real enemy is the attachment to sin, which can bring about the failure of our existence".
Thus, whereas the Times article suggests that the Pope claimed that hell was a place where sinners really burn in fire, the Guardian article suggests nothing of it, and explicitly says that the Pope "failed to elaborate on what lay ahead for the sinner in the afterlife," and says he added only the bit about attachment to sin. It later says that he was "short on details about hell," "has declined to paint a picture of hell," and so forth. This is a very different account.
(4) Examine the clues found in the context presented in the article. One of the strengths of the Times article is that it gives the comments of "Vatican officials" on what the Pope said; and it summarizes them as suggesting that (at least part of) the Pope was trying to do was "to reinforce the new Catholic catechism." When reading a news article, it's often a good idea to regard it less as a statement of the facts and more as a collection of clues thought to be relevant to understanding an event. This link to the Catechism is a clue, and a potentially significant one; it shows that there is a certain authority, namely, unnamed Vatican officials, and that this authority has indicated that the Pope intended to do something in making these claims. This allows the reader to do two things: weigh the credibility of the authority making the comment, and, if they are interested, follow the thread provided by the authority (in this case, the relevant sections of the Catechism). The article provides a number of other clues, devoting four paragraphs, for instance, to the comments of a Church historian, one to the views of the Pope's predecessor, and one to the current Pope's claims about limbo.
Turn to the Guardian, and you have a very different set of clues. While that article gives four paragraphs to a dean of theology, it also gives three paragraphs to the Pope's involvement in political debate and one to his claims, as a Cardinal, about the devil. Actually, it's clear that this article includes an argument; one could argue that there's a buried lede here, because the article suggests that these claims are part of a general pattern in which the Pope pushes for a "back-to-basics view of religion and society that has spilled over into political debate in Italy and beyond." Several bits of evidence are provided in favor of this view. Whether or not one considers this a buried lede, it is something worth noting, since, if the argument can survive examination, it would shed interesting light on the whole issue.
In any case, the articles provide critical inquirers with several suggested lines of investigation, should they wish to follow up on a particular point. Obviously, how much anyone can follow up on them is a matter of time, resources, and interest. Any critical inquirer has to engage in a bit of cost-of-inquiry reasoning -- asking themselves the practical question of what they can seriously follow up, and what they can't, what (if anything) they can do about the fact that they can't, and what qualifications they have to apply to their conclusions when they can't. But news articles are generally starting-points for further inquiry, collections of clues for investigation, signs indicating where further evidence can be found, and the critical reader of news articles will treat them as such. At least, good journalists make them so.
Those are four that occur to me off-hand. I'm sure there are more. Any suggestions for adding to the list?