Implementing one of the suggestions from http://code.google.com/p/google-diff-match-patch/wiki/Plaintext

google-match-patch structured

var dmp = new diff_match_patch();

var text1 = "your input text source";
var text2 = "your input text destination";

var current_unicode = parseInt('2000',16);
var charmap = {};

var replaceFirstTag = function(str,code) {
	var nu = code+1;
	while (charmap.hasOwnProperty(String.fromCharCode(code.toString(16)))) code++;
	var char = String.fromCharCode(code.toString(16));
	var sp = str.search(/</);
	var ep = str.search(/>/);
	var tag = str.slice(sp,ep+1);
	return [str.replace(/<.*?>/,char),char,tag];
}

while (text1.regexIndexOf(/<.*?>/,0) > 0) {
	var replaced = replaceFirstTag(text1,current_unicode);
	text1 = replaced[0];
	text2 = text2.replace(replaced[2],replaced[1]); // also make the same substitution in the second text!
	charmap[replaced[1]] = replaced[2];
	current_unicode++;
}

while (text2.regexIndexOf(/<.*?>/,0) > 0) {
	var replaced = replaceFirstTag(text2,current_unicode);
	text2 = replaced[0];
	charmap[replaced[1]] = replaced[2];
	current_unicode++;
}


var d = dmp.diff_lineMode_(text1, text2);
dmp.diff_cleanupSemantic(d);

var rendered = dmp.diff_prettyHtml(d);

for (char in charmap) {
	var re = new RegExp(char,"g");
	rendered = rendered.replace(re,charmap[char]);
}

// rendered is the final product