I really don't think most people care that the Abrams films weren't a clean reboot. It's not that big of an issue.
It was structured that way because the writers were fans and wanted to tell an unfettered story about Trek without trampling all over established Trek. This was done out of respect for Trek and its fan base.
And it was answered with vitriol, wailing and gnashing of teeth from Trek purists everywhere.
The old adage of not pleasing all of the people all of the time goes double for cult fan bases like Trek. It's better to simply ignore their requests, entreaties and feelings since the level of rage will be roughly equivalent no matter what you do.