Initiating combat in Eclipse
Combat will always take place. If you are in a diplomatic relationship with another player, that relationship is broken the moment one player enters a hex occupied by the other player. This is covered on p11 of the rules:


  Your Diplomatic relations  stay in
  effect until the end of the game, unless you attack  one of the
  players you have Diplomatic relations with, or  they attack you.
  Moving your Ships to a hex where the other player has a disc or a Ship
  is also considered an attack. Both players then return the Ambassador
  Tiles and cubes  to the owner. The cube goes back to a Population
  Track,  chosen freely by the owner


There is no possible way to pass through a player's hex without any combat, because of pinning. p14 says:


  If your Ships move into a hex, or out from a hex, containing  other
  players’ or Ancient Ships, at least one Ship per each  opposing Ship
  must stay (the Ship is said to be "pinned")  and engage in combat in
  the Combat Phase


So the only way you can move a ship through another player's hex is if you already have 1 ship in that hex per opponent's ship in that hex.