As you noticed, the highlighting of fields is an user preference. Therefore, changing the setting behind the user's back is considered to be "not nice".
However, there is a way which is accepted:
• you create a simple document-level script (note that when you add it, you will delete the function definition, and then add the text):
var rths = app.runtimeHighlight ;
app.runtimeHighlight = false ;
• in the willClose Document JavaScript, you will add:
app.runtimeHighlight = rths ;
And that should do it. You are saving the user's setting in the variable rths, and when you close the document, you reset it.
Hope this can help.
Max Wyss.