What would I suggest for the other side's unused wire?

Pull it back up into the engine compartment and leave it.

This can be funny on two different levels.

1st level: If sometime down the road you happen across this connector and forget what the heck its used for.

2nd level: If you ever sell your Xj and the next guy happens upon it. He will have NO CLUE what the heck the DAPO had that wire there for.