I have to give the writers credit once again for sticking with their guns. Now that angels of the Lord are a part of the mythos, the characters discuss them at length and try to work out their place in the order of things. It's the same discussion that the fans have had since the revelation at the end of the premiere, and the explanations fit without too much trouble.
In essence, the hunters have never heard of angelic intervention because, quite simply, there hasn't been any. According to Casstiel, the angels aren't deployed until the situation gets apocalyptic and there's a possibility that Lucifer might actually be released. Lilith and her demonic followers are making just such a move, opening a total of 66 seals to accomplish the task.
None of the action quite fits with the Book of Revelation, but it's enough to communicate how the war has escalated. It might also begin to explain why Dean was delivered out of Hell to do God's work. Regardless of the circumstances, the Brothers Winchester unleashed the demons on Earth at the end of the second season. That included Lilith, who has started this latest mess and forced the angels to war. Whether or not Azazel had this in mind from the start, Sam and Dean bear some responsibility to make things right. This was the interpretation that Gordon and others followed early in the third season.
I still think this will involve each brother making use of their respective resources. The easiest way to undercut Lilith would be for Sam to assume his mantle as Antichrist Superstar. He still has Ruby and her training in his back pocket. And I still think Dean has untapped abilities as well, perhaps as a side effect of his relationship with Casstiel. That said, if this is becoming a truly cosmic battle between God and Lucifer, then all bets are off the table.
Taking the wide view, while Dean's questions touch on the pulse of so many in the world, especially in tough times, it makes sense for God to hold back. For one thing, if the presence of an angel can do the kind of damage seen in the premiere, God's direct intervention would be even more powerful. Besides, it's a question of scale. The hunters were fighting former humans converted into demons. When the bigger demons came out and Lilith went after the seals, that represented an escalation: the big guns had to come out to match the forces of darkness. As the Book of Revelation makes clear, the headliners don't throw down until the endgame.
None of which would matter if it didn't come down to what "Supernatural" does best: character. Dean is still struggling with his long-standing atheism, and we're beginning to see some cracks in his hyper-defensive stance. At this point, with the issues surrounding the CW, the writers can afford to take chances and explore matters of faith in more depth. Dean is usually the less emotive brother, so this is a real opportunity.
Both brothers (and Bobby, for that matter) get to show their deep sorrow and horror for the consequences of their chosen profession. That said, I think they're taking on too much responsibility on their own shoulders. All of those deaths were caused by the demons and monsters that the Winchesters and Bobby sought to kill. The objective truth is that there would be a lot more death and suffering had the hunters never acted in the first place.
But I also believe that it is that very human quality of assuming guilt that keeps the Brothers Winchester grounded. They've always taken responsibility for things out of their control. It also continues to drive them to stop more from happening. We've seen others (like Gordon, for example) who have lost perspective. It's hard to watch Sam and Dean take the accusations of their "victims", but they wouldn't be our heroes if they didn't.