It's very interesting to me that Sam and Dean have never succeeded in killing a witch.
In Malleus Maleficarum, Great Pumpkin and Criss Angel, the witches are killed by others (Dean did kill Tammy, but she was a demon, not a witch.) In the Curious Case of Dean Winchester and Shut Up, Dr. Phil, the Winchesters tried to destroy their magic and kill them, but failed, and ended up doing damage control instead. In Body Swap, they just let them go when it looked like they had learned their lesson.
It's realistic that they don't manage to gank every single foe, and it's consistent that the same type of foe keeps thwarting them. It's like a particular kind of enemy manages to exploit the same chink in their armour. Witches are human, so on a psychological level, it's harder to kill them than something non-human. But also their magical powers seem to thwart the boys with their sawed-off shotgun methods. It's like they're Barbarians in the Dungeons and Drangons world: they're extremely badass, but they just can't deal with magic. And this fits with what Kripke envisioned for them, from the start he said they were going to fight with chainsaws rather than with wands. Some might question why they let the witches go, but they didn't really. They tried to kill them and failed, so they had to resort to Plan B.
And what a Plan B it was! The concept of the Winchesters playing Dr. Phil to a couple of witches lashing out in the throes of marital woes was absolutely hilarious, and that scene played out beautifully. Cordelia and Spike were tremendous in the roles, and it was so funny to watch them air out dirty laundry going back to Columbus while intermittently using their powers on Sam and Dean. (The scene was great, the only thing that could have made it better is if there had been more fanciful magic like the bees, rather than just slamming the boys around.) It was actually a smart move to reconcile them to stop them from doing more damage—because from the looks of things, they were actually doing good things for the town through their charity and development work until their relationship hit the rocks. Witches can be like tricksters in a way, chaotic neutral rather than outright evil. (I love me some tricksters!) And I'm actually kind of glad the Starks weren't killed in the end, because I really hope they come back! And seeing as they're the only thing that has even slowed down the Leviathans so far, they'd be handy to have around.
It was also good for Sam and Dean that they didn't kill the Starks, because otherwise the Leviathan on their tail would've killed them. I liked the way that was built up and played out. It kept the Leviathan threat alive, and set us up for more trouble with them. Big Trouble, I'm sure. I'm looking forward to seeing what the Leviathans have up their sleeve.
I have to add that, although at first glimpse, it might seem a contradiction for Dean to kill the kitsune but not the witches, that if you look at the bigger picture instead of just the last few episodes, it is actually pretty consistent. (Actually, even within the last few episodes it's still not all that contradictory, for although he did kill a kitsune, he also let a kitsune go.)
First of all, they didn't decide to let the witches go: they tried to kill them, got their bums kicked, and only then resorted to damage control.
Secondly, as I have said, they have never killed a witch, and have let witches go on a couple of occasions before, in Swap Meat and the Curious Case of Dean Winchester. There is a fundamental difference here: the kitsune was a supernatural creature, the witches are human--and Dean and Sam have always shown a reluctance to kill humans. They have always shown a preference for stopping witches rather than ganking them. As the Starks had actually been do-gooders before their marital meltdown, it is legitimate to hope they will go back to that, and come back and try and kill them again if necessary. Sometimes, they let people off with a "Be good, or we'll be back." And Sam and Dean have bigger fish to fry with the Leviathans at the moment, and when someone has just saved your life, it doesn't seem like the right time to gank them.
They have even sometimes let supernatural creatures go, even though they have killed before and will likely kill again, as happened with Lenore and her nest, and the kitsune boy just a few weeks ago. He cannot survive without human pituitary glands, and he's too young to work as a mortician, so chances are good he will kill. For starters, he has sworn to kill Dean himself. It's a very grey area, rather than black and white. And saying it was black with the kitsune and white with the witches ignores the bigger picture and the shades of grey.