OK, I couldn't resist to dig into this.
I am having partial success by overrriding the 
function _jmolDocumentWrite(text) 
present in Jmol.js, with a new definition:

Add this to the header of your page AFTER the call to Jmol.js:
<script type="text/javascript">
function _jmolDocumentWrite(text) 
{       // Override Jmol.js
  if (_jmol.currentDocument)
  {  //_jmol.currentDocument.write(text); //this is what Jmol.js uses
     /* This is the new code, slightly adapted (A.H.) from 
                the addElement() function at  
https://developer.mozilla.org/en/document.createElement
                LICENSE: Code samples in MDC wikis are available under the 
terms of 
                the MIT License, 
http://www.ibiblio.org/pub/Linux/LICENSES/mit.license
         */
        // 1. Create a new div element and give it some content:
        var newDivForJmolJs = document.createElement("span");
        newDivForJmolJs.innerHTML = text;
        // 2. Add the newly created element and it's content into the DOM:
        document.body.insertBefore(newDivForJmolJs, null);
        // (Firefox and Opera require the 2nd argument, even if null)
  }
  return text;
}
</script>

jmolApplet() works (Firefox, Opera, Chrome, Safari, all in WinXP)
jmolLink() work
jmolButton(), jmolRadioGroup() and jmolMenu(): depends on the browser




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