It won't be ND's choice someday unless they either remain independent at a lower level DI or they can get Navy into the Super ACC ahead of UConn, Temple, WVU, UCF and USF.
There are a number of ways ND can continue playing Navy in a "super conference" world. Don't forget, Notre Dame ALREADY has special rules that don't require them to be a full ACC member in order to get Power 5 considerations. Options for continuing to play Navy post-realignment:
1. "Power 5" exemption for FBS independents. BYU, Notre Dame, Navy, and Army "count" as Power 5 teams.
2. A one-game exemption for existing agreements. The rule could read "Power 5 schools must only schedule other Power 5 opponents except for agreements already in place at the time of ratification." ND and Navy officially make their agreement "perpetual" and they're set.
3. Navy membership in the ACC.
4. A sixth power conference. There are enough competitive teams (several from the American) out there to form one more, IMO.
5. A thirteenth game outside of the "regular season". It might have to be billed as an exhibition or something like that, but it could happen.
Note that none of these options involve Notre Dame fully joining a conference or being relegated to any kind of Division 1-and-a-half. No matter what happens with future realignment, Notre Dame will always have a seat at the table. There's no way that the new "power 5 NCAA," whatever it will be called, unilaterally dictates that we'll never again see Notre Dame - USC, Notre Dame - Stanford, Notre Dame - Navy, Notre Dame - Big 10 unless Notre Dame joins a conference in full. Just ain't gonna happen.