iText (and iText_Sharp_) are quite capable of adding JS to an existing PDF... page actions, links, document level script, you name it.
The JavaDoc can be found here.
This was written with Java in mind, but the C# code would look almost identical (if not exactly the same, with the exception handling stripped out like this).
PdfReader myReader = new PdfReader( myFilePath ); // throws IOException
PdfStamper myStamper = new PdfStamper( myReader, new FileOutputStream(outPath) ); // throws IOE, DocumentException
// add a document script
myStamper.addJavaScript( myScriptString );
// add a page-open script, 1 is the first page, not zero0
PdfAction jsAction = PdfAction.javaScript( someScriptString );
myStamper.setPageAction( PdfWriter.PAGE_OPEN, jsAction, myStamper.getWriter(), pageNumber ); // throws PdfException (for bad first param)
PdfFormField button = PdfFormField.createButton(myWriter, PdfFormField.FF_PUSHBUTTON);
button.setWidget( myRectangle, PdfAnnotation.HIGHLIGHT_INVERT );
// the important part, adding jsAction
jsAction = PdfAction.javaScript( buttonScriptString );
button.setAdditionalActions( PdfAnnotation.AA_DOWN, jsAction ); // mouse down
myStamper.addAnnotation( pageNum, button );
myStamper.close(); // write everything out, throws DocumentException, IOE