I don't subscribe to him being in their for a lot longer. I just think the result of the Heresy, the defeat and subsequent events justify his change just fine. I've never been an Abaddon fanboy either. I didn't like him much at all before ToH, still not a Abby fanboy. I want to read more of Khayon and Lheor.
As for the cloning theory. I've personally hates that theory ever since I first heard it.