As long the generator doesn't provide an option to handle this and as far I have noticed XHTML compatible output is generated, a small XSLT transformation could be used, instead of replacing all the < > (and maybe further entities) by hand.
I was stumbling over the same problem when generating my own HTML reports directly from exported XMI.
Here's a snippet to replace the entities:
<xsl:template name="preserveTags">
<xsl:param name="text" />
<xsl:variable name="tmp1">
<xsl:value-of select="replace($text,'&amp;lt;','<')" />
</xsl:variable>
<xsl:variable name="tmp2">
<xsl:value-of select="replace($tmp1,'&lt;','<')" />
</xsl:variable>
<xsl:variable name="tmp3">
<xsl:value-of select="replace($tmp2,'&amp;gt;','>')" />
</xsl:variable>
<xsl:variable name="tmp4">
<xsl:value-of select="replace($tmp3,'&gt;','>')" />
</xsl:variable>
<xsl:variable name="tmp5">
<xsl:value-of select="replace($tmp4,'&quot;','"')" />
</xsl:variable>
<xsl:value-of disable-output-escaping="yes" select="$tmp5" />
</xsl:template>
Take care which XSLT-processor you're using, this is XSLT2.0. At least with Saxon9.1 it works fine.
In general I agree, the EA HTML generator should provide such option.
Allowing to post process the output with a stylesheet like the XMI Export would also be a good idea (BTW: That XMI-Export option didn't work with my XSLT, so I'm starting the postprocessing manually).
HTH
Günther