I have created a simple command line utility to convert a Balsamiq Mockups BMPR file to JSON. It is really basic and far from completion, but if you are interested in trying it out, here is the link:
You can download the pre-built binary directly from this link:
It basically extracts the contents of the BMPR file and emits a JSON file. Which may be useful for integrating with diff tools, or to quickly inspect the contents.
EDIT: Another thing, if you use Beyond Compare then you can import a pre-packaged file format that I have prepared here:
This will add the converter and grammar for JSON to Beyond Compare so that you are ready to compare BMPR files