that's how i saw it too. they are well aware that jesse is there, and that walt is there.
i don't think they are killing everyone. they need someone to cook their meth, so they are going to take either jesse, walt, or both.
hank and gomez are definitely toast.
jesse was getting out of the car last time we saw him. i have no clue what happens to him, but my best guess is uncle jack takes jesse hostage as a cook, and they leave walt alone, since, you know, he was just arrested. but since walt's evidence has suddenly dissapeared, he isn't arrested, and he dissapears to settle the score and save jesse.