Obviously, it's impossible to say exactly what Lucas was thinking, but there are some hints in very early drafts of The Empire Strikes Back that when he originally wrote the line he didn't think it would refer to Leia.
The very first Empire draft was written by Leigh Brackett in 1977 and annotated by Lucas. In this draft, Vader is not Luke's father, he actually killed Luke's Father. In one scene, Luke summons the spirit of Ben, and he brings the spirit of the elder Skywalker:
Brackett named this sister "Nellith", and Luke's father says they're "far apart" for safety, so there's the impression this isn't a character we've met.
In the very next draft (wholly written by Lucas), Vader became Luke's father, and this scene vanished. But there's a quote from an interview with Empire producer Gary Kurtz:
"[Leia]'s not his sister that dropped in to wrap up everything neatly. His sister was someone else way over on the other side of the galaxy and she wasn’t going to show up until the next episode."
So perhaps Lucas was still thinking about this idea -- a sister hidden on the other side of the galaxy -- when he wrote the "there is another" line in the final draft. This is probably the closest you'll get to an answer.
A little more detail and scans of the entire scene from that first draft available here. And there's even a PDF of Brackett's entire draft, complete with Yoda named "Minch", Han never being frozen, Lando "Kadar", and other weird stuff.