It was never intended as the truth. They filmed the scene with David Prowse speaking that line and Mark Hamill reacting to it, but Lucas and Kershner had always intended to replace Prowse's dialog with James Earl Jones' correct line.
From an interview with Hamill:
But, for example, your big scene, one of the classic cinematic moments when Darth Vader divulges his true identity, is no longer a revelation.
It's such a great moment! The fake line that was put in there just to try and keep the secret was "You don't know the truth: Obi-Wan killed your father!" But as much as I enjoyed leaking false information, it was a wonderfully hard secret to keep because (Irvin) Kershner, the director, brought me aside and said "Now I know this, and George knows this, and now you're going to know this, but if you tell anybody, and that means Carrie or Harrison, or anybody, we're going to know who it is because we know who knows."
The annotated screenplays discuss some of the history of these plans. The idea of the two being related dates back to at least the second draft of Empire.
George Lucas: "I didn't discuss the notion of Vader being Luke's father with Leigh Brackett. At that point, I wasn't sure if I was going to include it in the script or reveal it in the third episode. I was going back and forth, and rather than confuse things for Leigh, I decided to keep the whole issue out of the mix. I figured I would add it later on."
The notion of Vader being Luke's father first appeared in the second draft. Vader became attracted to the dark side while he was training to become a Jedi. He became a Jedi and killed most of the Jedi Knights; very few escaped.