In Terminator: Genisys, Kyle Reese was sent back in time but didn't have a child with Sarah Connor within that timeline.
How is John Connor alive if Kyle and Sarah didn't get together in 1984?
As the movie explains, time travelers experience multiple time lines when traveling, in a super imposed state (Schroeder's Cat principal). Kyle experienced and remembered the original Cyberdyne timeline and the new Genisys timeline. Since both time lines exist until a definitive event happens in real time. Before that happens, Infected John is sent back. It's a very flexible future until something forces it one way or the other. It does not follow the predestination theory of time travel.
It's almost impossible to avoid these things with movies' time travel. At the end of T2, we believe that the Judgement Day was avoided, but then who sent Kyle Resse back in time to father John Connor to stop the whole thing? It's similar here.
One could argue that John is Sarah's and Kyle's son from a parallel (in our terms: original) timeline. Like the timeline split in "Back to the Future 2 and 3".
Or, maybe they will have John later on. We saw during the credits that Skynet isn't dead, so what's stopping us from having the original(ish) timeline, just shifted 34 years forward (because John is conceived in 2017 instead of in 1984)?