Lowering the comprssion ratio can be done in a few different ways.
As menioned you can change the pistons. You could also increase the volume of the compression chambers in the head, or fit a thicker head gasket.
I would be inclined to calculate what the compression ratio is using the parts you have before doing anything rash. Has your engine builder done this already?
Below are a couple of pages that might help you if you want to learn a bit more about what the compression ratio is and how to calculate it:.
http://en.wikipedia.org/wiki/Compression_ratio
http://www.rbracing-rsr.com/compstaticcalc.html