interpret Leonard Nimoy's character in ST09 as being from a different timeline than the Prime Timeline. If you just really can't stand the idea that ST09's timeline branches off from the regular timeline.
But that's not the creator's intent, and it's not the interpretation the licensed tie-ins are going to use. The tie-ins are going to obey the instructions on what is canonical from the people who run canonical Star Trek
-- which is, right now, J.J. Abrams and company.
As far as the Alternate Timeline Federation developing its own DTI...
I wouldn't be surprised if the events of ST09 lead to the establishment of their own DTI. There probably wouldn't be one yet as of 2258 -- no one knew that there was a temporal incursion in 2233 when the Narada
destroyed the starship Kelvin
until Kirk encountered Spock Prime in 2258 and Spock Prime revealed the Narada
's future origins.
But.... Given that the events of 2258 involve the most devastating attack the Federation has yet suffered in the destruction of Vulcan, the destruction of all Federation starships and starbases in Vulcan orbit, the attack on Starfleet Headquarters on Earth, and the deaths of 6,000,000 Federates, I wouldn't be surprised if the institutional culture, if the ethos, of the Alternate Timeline's Federation DTI equivalent ends up being a great deal more militant, more controlling, of temporal events. That doesn't HAVE to be the case, but obviously the events leading to the discovery of time travel in ST09 were a great deal more traumatic for the Federation than the events leading to the discovery of time travel seen in TOS and Forgotten History