This should be relatively efficient:
<xsl:variable name="unique_hrefs" select="distinct-values(//xref/@href)"/>
<xsl:template match="p">
<xsl:element name="{local-name()}"><xsl:apply-templates/></xsl:element>
</xsl:template>
<xsl:template match="xref">
<a href="{@href}">
<sup>
<xsl:value-of select="index-of($unique_hrefs, @href)"/>
</sup>
</a>
</xsl:template>
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