Setting the fillColor property to null should do it..

Example of removing the fill color of the first selected path:

var paths = document.getItems({
	type: Path,
	selected: true
});

if (paths.length > 0) {
	paths[0].fillColor = null;
}

Please post your code if you still can't get it to work, you're probably making a mistake somewhere else.

this the basic version:

var myPath = new Path();
myPath.strokeColor = '#000000';
myPath.strokeWidth = .2;
myPath.fillColor = null;
myPath.add(new Point(x,y));  etc. etc.

... trying to avoid the user's fill colour at the time of running the script being used as the fill

Well your code works for me.. I don't get a fill...