I know you said that the microchip would be harder to remove than a label, but am afraid that could be costly.
Did you catch the thread on QR codes and making them on your label? You can do it for free, and it is very easy.
http://www.quiltingboard.com/t-121655-1.htm here is how to print a code, so any cell phone (with the app) can read it. If you sew the label into the quilt, so that it would be hard to remove, it would help.
I have also heard of making an extra label inside the binding. So, if you see your lost/stolen quilt, you still have proof it is yours, even if they have removed the label.