I was on a diversion earlier this year (mechanical in this case) that lead to much the same scenario. I called the mileage plus help desk after a week or so had passed and they manually forced credit for the diverted leg (in this case ORD-FRA diverted to BOS). I got credit for the ORD-BOS segment and it posted under the original flight number. I doubt you could make the case that you should get credit for the original routing which was not flown. Lastly, I should point out that this all happened under the pmUA computer system, so no guarentees they can make it happen now that Shares is in place!