I loved the ending, don't think the books would have been as memorable if that hadn't happened - it's pretty emotional. I'm just glad we're getting a book about Will after this has happened sometime in the future and we're got a few books about Lyra when she's older.
As for the Spectres, the subtle knife drives them away so they'd probably flee before Will could swipe at them. Second, the Spectres might not appear instantly out of the window (?) but could be formed afterwards, perhaps when the knife bearer has moved along (but that's never mentioned to be true, just a suggestion). Killing Spectres is also questionable, when Xaphania talked about them, she said she would take care of them. As they are a part of the Abyss, a part of darkness, a part of nothingness and all they eat is Dust and they have no real substance, can they really be killed? When Xaphania went to kill the Spectres, she didn't ask for the knife so perhaps the knife couldn't kill them, it was just something that could cut them/remove the Dust from them or they were just generally frightened.
I don't think they really could kill a Spectre, the only way to get rid of one would be to send it down the Abyss again.