The more I think about it, the more I'm convinced that Christian Shepherd absolutely, positively has to be alive. Okay, maybe not "absolutely, positively," but I'm pretty sure and here's why. We know from the newspaper that the events of the flash forward take place in 2007. If this were the same reality they left, that would make three years since Jack accused his father of malpractice, prompting the latter to flee to Australia, where he died. At a minimum, therefore, the "new chief of surgery" couldn't be replacing Christian in that position, which would have been filled shortly after the latter vacated his post in 2004.
Some skeptics argue that Jack's reference to his father being "upstairs" was the ranting of an addict. As messed up as Jack seemed to be, he didn't strike me as so out of his mind that he'd forget his father was dead. Others apparently felt the same way -- Jack hadn't been stripped of his access to the hospital or his medical license so far as we're aware. Indeed, the new chief of surgery felt compelled to use exhaustion from the accident as an excuse to deny Jack's demand to operate. If Jack had been stripped of his operating privileges, the chief would have said so, end of story.
What cements it for me, however, is Jack's encounter at the pharmacy. Let's recall what happens, keeping in mind that Christian would have been dead for three years at this point. Jack has a dispute with the pharmacist, who refuses to fill his prescription after checking it on the computer against some kind of electronic database. Jack then presents her with Christian's scrip, which she says she'll have to verify by phone with Christian's office. But even if she hadn't telephoned -- and this is key -- she still would have checked the prescription against the same electronic database that she did with the first. And that database almost certainly would show if Christian were three years dead. Ergo, the Christian resurrection!