I find it's actually a bit of a pain in the butt, especially on an admin screen I have on one of my sites which allows me to edit a users details. Everytime I load the page, it puts in MY details instead.
The only way that I can think of doing it is that what you can do is load the page with data in, and then once it has loaded check to see if the data has already been altered. If it has, just display a warning to the user, telling them about this "feature"
Here's a quick test page (that works, might I add):
<html>
<head><title>Autofill</title>
<script language="Javascript">
function check(){
if(document.getElementById('username').value != 'dave'){
alert('You currently have the autofill feature turned ON. This could alter the way that this application works.\n It would be beneficial to you to turn it off.');
}
}
</script>
</head>
<body onload="check();">
<form action="#" method="GET">
Password: <input type="password" id="password" name="password" value="oasss"><br>
Username: <input type="text" id="username" name="username" value="dave"><br>
<input type="submit" value="Submit">
</form>
</body>
</html>