I think your allergy cure worked beautifully and the ear infection is a totally unrelated (although sucky) event. I had ear infections all the time when I was a kid and spent a lot of time swimming in either the ocean or a public pool. They can cause permanent hearing damage and so are not to be taken lightly.
I'd say, if it doesn't clear up soon on it's own, suck up the non-Primalness and get the antibiotics. Then get your system back on track agin afterward with some more yoghurt.