My husband and I fly like this all the time, and the person in the middle does not realize we are together until the end of the flight, when we stand and start talking about where we are meeting up. But, neither one of us is afraid of flying.
In your case, I think you really need to have him seated next to you, and the aisle is probably the best seat for you. Although I think it will cause some confusion at first, I think you may need to ask the person seated in the middle if they would like to move to the window. If they do not want the window, you may have to move to the window or middle.