What kind of confrontation could Luke have that would not result in him fighting Vader? Was he just supposed to incapacitate him? Was he supposed to talk to him and then carry on with the rebels?
Luke tells Obi Wan "I can’t kill my own father."
Obi Wan says "Then the Emperor has already won."
The killing part was Luke’s idea. Obi Wan is responding to his hesitancy to confront Vader, not whether or not he should kill him. He has to be willing to kill him if need arises, because that’s what a confrontation means (especially with lightsabers.)
YODA : Away put your weapon.
BEN : It’s your father’s Lightsaber.
YODA : Your weapons, you will not need them
BEN : (the quote you use).
Yoda isn’t interested in Luke confronting Vader as a military target.
He wan’ts Luke to confront his fear and conquer it. His fear is he will become Vader and he almost does by following Ben’s line of thinking. Instead (going by the sequels) he becomes Ben which is a bit of a shame.