So what's your actual question? How to make peace between your father and your wife? Or how to proceed with your son's diet?
That phone conversation in itself doesn't sound too mysterious - it's very well possible that he honestly thought that he was just stating his concerns, but that he did so in a tone that sounded very accusing to your wife. It doesn't matter whether or not one of them is 'right' or 'wrong' about what was said; it does matter that your wife feels hurt. So get him to apologize to her; surely he must understand that he hurt her feelings even if he didn't intend to do so? Do not ask her to approach your father - if my husband asked me to do that, I'd feel he chose his father's side, not mine. Your father has been told that he was misunderstood, so it's for him to take action.
Regarding your son's diet: it's your son, so you and your wife get to decide, especially since this is a medical issue. Your parents don't have a say in this matter.
By the way (can't believe I didn't notice this earlier): do you mean Christmas Eve 2013? Has this really gone on for nearly a year!?