[@Angel Vicky]

Oh, God no. He'd love a good ol' apocalypse - and was quite happy killing anyone who got in the way of that; including angels. So he would not be happy with our work.
The way I'm having it is that Heaven does actually know about the whole stopping-the-seals thing, but in order to keep their naive underlings (Such as Castiel) obeying their orders, they're pretending to support our actions: much like they did with the Winchesters.
However, they don't know who or what brought this second group together. And after a few successes on our part, they'll begin to get rather impatient with us.