You know, I myself have run into this problem several times. Booleans are useful, but sometimes not practical. It's really hard to get them to work, especially on objects with complex topology. You should be able to somehow attach a circular CV curve or a basic Nurbs curve to an object or specific face and have it form a face when it does. The problem with the polygon make hole tool is that the object you select to make the hole has to be a face from the original object, which if I am correct, doesn't allow you to modify the face how you want. Arr!