I would use plastic from a CD case, that is about as clear plastic gets and it polishes well, too. As Fermis said, cut the hole larger so you can put in a larger than necessary piece of clear, let it stick above the plastic surface, and sand and polish to conform to the skin. Mask to the size of the window and paint.
I have used clear epoxy on small windows with good results but you do have to be careful to not entrain air. I apply the epoxy just like white glue, with a toothpick and work from the outside in. I put in the epoxy from inside the window and just let it sag outside. If not enough epoxy is applied the first time you can add more in layers and it will not be visible. It takes awhile to harden, (as much as a week) but when it is cured it can be sanded back to conform to the outside skin. I did the windows on my DH-125 with this method.