I'm sure you're right. I assume that Apparate is from a similar root to the word appear, and Disapparate is similar to disappear.

However, in general, we talk about to Apparate and mean both halves of the process. I'd probably use Apparate in the sentence you have given because although she's talking about disappearing from where she is, it's also implied that she's Apparating to Theo. I'd tend to use Disapparating where the scene ends with someone dematerialising with no mention of where they go to.