If you have proper closing tags in your document then calibre *will not* insert tags of its own. For example convert eh following html:
Code:
<html>
<body>
<p>A <span>span</span> tag.</p>
</body>
</html>
And you will get
Code:
<?xml version='1.0' encoding='utf-8'?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head><title>Unknown</title><meta content="http://www.w3.org/1999/xhtml; charset=utf-8" http-equiv="Content-Type"/><link href="stylesheet.css" type="text/css" rel="stylesheet"/><style type="text/css">
@page { margin-bottom: 5.000000pt; margin-top: 5.000000pt; }</style></head><body class="calibre">
<p class="calibre1">A <span>span</span> tag.</p>
</body>
</html>