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The world has moved on from XML. You need to stop clinging to XML in your workflows. A serious publishing tool, as you put it, should deal with actual, real-world HTML and produce code that is tested to work in actual real world software, rather than a DTD/spec that is a guarantee of precisely nothing.
A <u> tag is a much nicer construct than <span style="text-decoration:underline"> which is what the epub 2 spec would require here. Not only is it nicer, it actually works everywhere and has the added advantage of allowing for easy customization of styles via CSS overrides. All a user has to do is add u { text-decoration: none} to turn off underlines. Which cannot be done with the style sttribute.
Sometimes you have to look beyond the spec and implement a solution that actually is superior than what t he spec recommends.
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