John's not sure what comes first on the to-do list, the relief or the gratitude or the yelling – at Dean for being an idiot and refusing to follow orders, at Ellen for letting him – and the door slams shut behind him while he's still making that decision, and he turns to storm towards the door – face like thunder, set in that stony 'John Winchester is pissed off' way - and catches sight of Jo and stops in his tracks.
She's been through the wringer (the voicemails had left out the specifics, but John's not an idiot) and Jesus, it shows, and that makes things simple because the anger flares again (at Walker and Kubrick and all the other sons-of-bitches, and at himself for dragging the boys into this life) and drowns everything else out – she was never supposed to be part of this, Bill would never have wanted....
There's the right thing to say, but as per usual that's elusive, and then there's the John way of doing things because damned if he knows what to do when the scrap of blonde he's used to thinking of as knee-high to a grasshopper and demanding candy and bedtime stories turns into a miniature woman, let alone what to say when said woman's been at the mercies of a psycho because, however indirectly, of all the things that are wrong with his family. She gets a nod, a gruff “Jo.”