I had the same initial reservations as you, but I have to say that having the bindings in the html and not hidden away in a JS file seems so much better to me, as the link between presentation and functionality is now completely obvious. It massively reduces the possibility of changing some HTML and breaking functionality because you weren't aware that someone had hooked up some javascript to an element using jQuery.
Also, as you point out, the use of the data-bind attribute does, I think, mean that it does adhere to the separation rule, though if you want to stick to it rigidly then make sure all bindings are to observables, computed or functions on your view model, don't use any code (i.e. a visible binding that checks the state of two observables). I'm not sure I'd take it that far though.