Knockout's perf on large re-renders is below average: http://mathieuancelin.github.io/js-repaint-perfs/knockout/ It also doesn't allow you to use programmatic render functions, nor does it have server-side rendering.
Vue 2.0's vdom implementation is mutation resistant - as long as you don't replace the element directly controlled by Vue (same as 1.0), the rendering will not run into problems. If you are really concerned you can always create a custom component that returns an empty element so that you can do arbitrary manipulations inside.