If you have a small cap style applied in ID.
Then you can open the xhtml files in textwrangler or another editor which does regular expressions (GREP)
search for what ever the line is, for example:
<p class="bodytext"><span class="smallcaps">This is the small caps</span>and this is the rest of the paragraph text</p>
Find/change in text editor
Find
<span class="smallcaps">(.*?)</span>
Replace
<span class="smallcaps">\U\1\l</span>
Then in your css you just need the
span.smallcaps{
font-size: 85%
}
This method "fakes" small caps by making the type uppercase but smaller