One form of protection for both you and your witness may be a legally-recognised, signed, witnessed statement: an affidavit. This kind of legal statement, initialled on every page and signed in the presence of a lawyer, is acceptable to courts in most countries and has important legal consequences. It signals that your source is willing to appear in court and provide evidence, if required. An affidavit should be given to a trustworthy lawyer for safekeeping. If your story results in legal challenge or action, the existence of the affidavit makes clear to anyone challenging it that your source is prepared to reveal herself if offered the protection of the court. It also protects you if your source later retracts the story.
Consider if having the affidavit will help your story. Your source may be spooked out by the formality of such legal documents, so perhaps broach the topic after you have gained his trust, or rely on other methods of protection such as extensive records and tape recordings.