A laudable intention on your part. However, unless I'm misreading your story, the updated script was not part of a product that your employer was selling. If that's the case, then your employer is within their rights to refuse to publish the improvements that you made. As hard as it may be to stomach, your lawyer gave you good advice: You did good by pursuing the issue, now let it go.

Your managers might also have started off with good intentions. Sadly, "We thought we could do this, but our lawyers told us otherwise" isn't a rare experience for managers in big companies.