First point: Oswin was not completely transformed into a Dalek, she was converted. This means that there is a part of her that is still purely Oswin. That is the part that has deluded herself that she is in her ship because she cannot handle being a Dalek.
Second point: Oswin was a genius and actually did hack all those systems within the Dalek defenses. She was not using a conventional intercom, she had taken over the speaker system and transmitting as she desired.
Therefore, because she was not communicating via an intercom, she was constructing the sounds passed through the speaker directly, and therefore could choose how she sounded. It makes sense that she would project the voice that she is most comfortable with. She seems to have gone through great lengths to maintain her humanity, and her projection of humanity. It only makes sense she would project her actual voice and not the Dalek voice she rejected.