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<summary type="xhtml">
<![cdata[
<div xmlns="http://www.w3.org/1999/xhtml">
my content
</div>
]]>
</summary>
<xsl:value-of select="atom:summary" disable-output-escaping="yes"/>
In this case I believe you can add a cdata-section-elements attribute to your <xsl:output /> definition to specify elements whose contents the parser should ignore.
Incidentally, if you want to preserve node structure, you wouldn't use <xsl:value-of />, but rather <xsl:copy-of />.