What about a simple XSLT that copies all of the XML forward except for the specific elements that you don't want?
You can use a modified identity transform and just add empty templates for the elements that you want to suppress.
For example:
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:template match="/">
<xsl:apply-templates/>
</xsl:template>
<!--Identity transform copies all nodes and attributes by default -->
<xsl:template match="@* | node()">
<xsl:copy>
<xsl:apply-templates />
</xsl:copy>
</xsl:template>
<!--Create an empty template for the elements that you want to suppress-->
<xsl:template match="ElementToRemove" />
</xsl:stylesheet>