If you want an even smaller (sans jQuery) JS highlighter that doesn't fail on edge cases, check my jQueryJSH: http://www.phoboslab.org/files/jquery-jsh/ github: https://github.com/phoboslab/jQuery-JSH
1) How do I know it doesn't fail on the same edge cases Prism might fail on? I see no tests. 2) Do you really need jQuery there? You seem to be using it only for the html method, and including 93K extra JS instead of just using innerHTML seems a bit overkill.
It checks for the case that .innerHTML setting is not supported (I think that was for certain versions of IE) and switches to using appendChild(). I think that that small oversight is somewhat reasonable justification for using a wrapper that abstracts away the browser differences, although it can be argued that once someone understands the differences, they could just add the use cases to their code.