Two questions here:
1) Would I be able to put an influence disk per influence action on a hex that is adjacent to one of my hexes, if the target hex is empty except for an ALLY'S ship?
2) If I leave an alliance while my ally has ship(s) in my hexes, is he considered a traitor because he "attacks" me?
Good questions. Here are some answers:
1) Yes. Ally's ships are not considered as enemy ships.
2) No. You become the traitor as the conflict happens because of your direct action.