There's a key difference between explicitly always knowing (which of course would make her a bit messed up to still follow through with 2 kisses in Empire) and "somehow" always knowing, which suggests to me that it's being considered more in hindsight. That she'd always sensed some kind of connection between them that wasn't romantic, but could never put her finger on what it was. This ties into her being force sensitive so it's all hunky dory to me.

Whether they should have even been siblings in the first place is another matter entirely though...