Nothing in the new film contradicts the existance of Enterprise, heck if you ask me the Xindi attack is likely a big reason why the Starfleet of this timeline is a lot more militaristic and advanced than the Real One.
There's no evidence that the Xindi attack didn't happen in the prime timeline. Until we're told differently, we can assume that it did.
Same goes for ST:FC. It was part of history all along. There was never a timeline where it did not. A classic predestination paradox. It always happened.