As submitted, Google Voice had several problems, including a massive privacy violation that would have held up any app. It is reasonable to think that they could have worked through those. The "duplicates the dialer, voicemail, and SMS" seems to be the key objection that Google could not, or chose not, to work around, but at least for voice calls that is changing as evidenced by Line2. I never saw SMS come up explicitly, but surely AT&T would not be happy to see that cash cow vanish. The question is if they had enough foresight and clout to get it protected in their agreement with Apple.
And, at least if you believe the statements to the FCC, AT&T has never had anything to do with the acceptance or rejection of the Google Voice app. So Apple ends up looking rather hypocritical here, when all of it's stated reasons for rejecting Google Voice also apply to Line2's app and yet that app was accepted.