I'm not sure, actually. Usually I'd say that it's just a retcon, but Paolini seems pretty damn keen on the idea of "If your parents are bad eggs, you must be bad! It's in the blood. It's that little set of double helixes that look like a scowling face."

Which, if it's true, possibly means that he always intended Brom to turn out to be the real dad - or, perhaps more likely, intended Morzan to be and then had a crisis because Morzan is bad, and Eragon isn't bad, but if Morzan is bad then Eragon must be bad. What to do?! Oh, Brom, Brom's good, he can be the father instead.

On another note: Paolini, Jeremy Kyle called. He has words for you.