I guess I don't see it as a huge issue. I appreciate the academies fielding teams, but it's not like either one has been relevant to the discussion in terms of a Big-6 Bowl in some time. Just deal with it on the rare occasion when it would happen. The selection committee could simply handle it "as needed".
While I understand the history and significance of the game, would it not be easier for the NCAA to simply agree to give Army/Navy an exclusive time slot a week or two earlier? Yes, I know the networks would not be happy but it seems like that could be worked out.