I don't even know why it's an issue, really. Abrams and his people said as much when the last movie came out four years ago. The classic Trek timeline and reality is still intact, but this new one just skews off of it to create a new series of events that they can play around with to make some great new stories.
As far as I'm concerned (since we're talking about a completely fictional universe here, anyways, where many basic scientific laws and simple logic never seem to apply to begin with) Data's head is still buried underneath San Francisco. It might never, ever be discovered in this alternate timeline and even if it does get found there might not ever be a positronic android built by Noonien Soong to contact and question about it and the thing might end up in a secret vault someplace along with other weird discoveries that nobody in Starfleet or Federation science can fully explain, but meh. It's probably still there.