There’s a somewhat spoilery interview from Joss Whedon with TV Guide Magazine regarding the upcoming storyline(s) for Dollhouse and it touches on Amy’s character; she will indeed be returning for those 2 other episodes! The relevant quote has been posted below.
Does Amy Acker return for more episodes? Is she still Saunders?
Amy Acker will return. We have two more episodes that we’re allowed to use her because of [her new ABC series] Happy Town. She comes back in an interesting fashion that I will in no way describe to you, a little bit later on. She’ll be the Doc, Claire Saunders. Where she’s been may be a surprise to people.