I don't see how that's a retcon or mistake, since it was established in book 1 the relative ages of those two Houses. Also, the point was not that Baratheons had universally dark hair, ignoring the eequally universal Lannister blonde, so much as the point that every marriage on record between a Baratheon and a Lannister produced exclusively dark-haired children. The point was that in 300 years, Joffrey was the first such child to have blonde hair. Also, subsequent histories imply the dark hair goes back even further. At the time of Aegon's Conquest, King Loren of House Lannister and King Agrilac of House Durrendon ruled from Casterly Rock & Storm's End, respectively. The first Baratheon married Agrilac's daughter and kepts his castle, lands, sigil and motto, with only the family name changing. Robert is as much a descendant of Agrilac as Tywin is from Loren. While the name might only go back to a bastard commander in service to the first Targaryen, the family can trace it's bloodline all the way back to ancient times when legendary heroes walked with gods, just as the Lannisters can. And as Orys Baratheon was rumored to have been the son of a Targaryen lord, it is even more likely that the black hair for which his descendants are famous was a inherited from his wife, of that ancient lineage.

Nothing in the later-released material contradicts the stuff in the first book of the series. If you need an example of retconning in Martin, you'll have to look elsewhere.