Her Heaven is perfect and her body destroyed, but that's no reason not to put her back on Earth.
After all, restoring her vessel can't be much different to all the times He has restored His wayward son. If anything her essence will be even simpler - the complexity that is Castiel was annihilated on a subatomic level, twice, whereas her soul is intact.
He starts with her skeleton, moulding each bone and carving out each socket. (He recalls watching the angel of solitude perform similar procedures on the man intended to be the Michael-sword, but it is different for Him. The body of Dean Winchester had still had a semblance of integrity, a base for the angel to work from, and Castiel had taken such care, whilst He must work mainly from His original description (and He had never been much good as a writer), and has no desire for the perfection His son had sought, for He does not share the same profound connection with the woman as the angel felt for the Righteous Man.)
Her organs are layered over the top, and the white table beneath her make her rebirth look like an autopsy. (Ironic, really. He should know, irony being one of the few things He was good at during His time on Earth.)
Blood vessels for this new vessel, and blood to flow through them. Skin layered over the top, unbroken and uncharred. Features reconstructed as though they had never been lost.
If He were not blessed (cursed?) to see the void where her soul should be but isn't, He could perhaps believe her to be sleeping.
Her soul is pristine, but it is not yet ready to be restored to her body. He cannot restore her to life as she was; in fact, were she not needed now He would happily let her rest in eternal bliss.
Adjustments must be made.
Her soul is reforged, made new, until it can no longer be called a soul. Instead, it is that celestial force that was His first creation, the one thing he never named. (Already it is producing her Grace, blue-white and pulsing softly; neither solid nor liquid nor gas)
He crafts her wings, flaming red to match her vessel's hair. She will be strong and fast, but still delicate. For now, she is the only angel in Heaven with functional wings.
And then the new seraph is pressed into her new vessel, and takes one shuddering breath. She has not breathed in months, hasn't been corporeal enough to do so.
Evil is coming. She will need her human talents, but her new abilities more so. The angels will be fully restored. Bonds will be broken and remade, and loyalties tested.
And He will return.
But not quite yet.
Now, he watches the table in the featureless white room as the angel Charlene opens her eyes.