There's no canon saying Kirk was *born* in Iowa, just that he's "from Iowa". Federation: 150 Years and The Autobiography of James T. Kirk (both set in the TOS timeline), have Jim born on the USS Kelvin en route to Earth. Then again, the script for ST'09 has Jim and Spock Prime compare notes on Delta Vega, where Spock says "you were born in Iowa" and Jim replies "I was born in space"
I think some of the "Prime timeline" talk was intended to keep a subset of fans from badmouthing something they hadn't seen for months on end and potentially killing part of the show's buzz.