Based on help from isherwood, used this as the solution:
With HTML tree like this:
<div><div><div class="highlightStart">highlightStart</div></div></div>
<div>Outside<div>Content to Highlight</div>More</div>
<div>second</div>
<div>third</div>
<div><div><div class="highlightEnd">highlightEnd</div></div></div>
This Javascript:
$(document).ready(function () {
$('.highlightStart').parent().parent().replaceWith("<div class='highlightStart'>");
$('.highlightEnd').parent().parent().replaceWith("<div class='highlightEnd'>");
$('.highlightStart').nextUntil('.highlightEnd').andSelf().wrapAll("<section class='highlight'>");
$('.highlightStart, .highlightEnd').remove();
});