According to director McG:
Kyle Reese must be kept alive, so he can be sent back in time from 2029 to protect Sarah Connor, impregnate her, and she'll give birth to John Connor, who will save us all. And the simplest way to understand that is to protect the triangle of Kyle, John and Sarah. Any deconstruction of that leads to more headache than satisfaction. [TerminatorChronicles.com]
In other words: Skynet already knows Kyle will travel back in time and become John's father. It also knows that in the near future, as a desperate measure, it will try to alter the past in its own favour. But in 2018, Skynet may not be ready yet to change the time-line, thinking it can still win in the traditional way. According to chaos theory, a chain of events is an extremely complex process, making the effects of altering the past impossible to predict: with Kyle dead and Connor completely removed from the time-line, perhaps someone else will become the leader of the Human Resistance, someone who might be even smarter and tougher than Connor. Skynet obviously didn't consider this when it sent the Terminators back to eliminate him, given that John & co. had breached its inner defenses and it was about to be destroyed anyway.
In one way of thinking, the best strategy for Skynet to win in 2018 is to lure Connor when he is rising to power, kill him and the Resistance leaders then, and leave the resistence in disarray. Another theory is that Skynet probably didn't want to cause a time paradox that would endanger itself: if it killed Kyle, the future of 2018 would be reset; John would not have been born and he wouldn't rise to be the Resistance leader, giving Skynet no reason to kill Kyle; the "predictable" future would cease to exist, and Skynet would have to start all over again and might even destroy itself in the process. It would be easier to kill Connor now and Skynet would win the war in 2018, instead of killing Kyle, resetting the future, and starting all over again. A third theory is that three different theories of time travel are used. In The Terminator
, they introduced the idea that time is static, like a train track. Everything that happened was meant to happen, and the outcome would be the same, no matter what the characters did. T2
introduced the idea of alternate realities. In this reality, Skynet was destroyed and then the characters could pick and choose their own futures, and the future of Kyle Reese would never exist. The third film used the idea that time is fluid, like a river. The events of the second film changed history, but couldn't rewrite it. Future events would still happen; they could be delayed, but never eliminated. The fourth film tries to go back to the idea of alternate realities, in that this future is different than Kyle Reese's original future, but it appears that there were so many plot holes, they're actually back to using the "time is fluid" idea.
Looking back at the events of the first two Terminator
films, we find that not only does John Connor send back his dad, to ensure his birth, but Skynet by default jump-starts its creation. If the Terminator was not sent to 1984, then Cyberdyne would never have gotten the Terminator arm and the CPU, and would not have started work on it. Skynet's creation was probably inevitable, like Judgment Day. The risk of no Connor runs the risk that the Terminator will not have had the influence on Cyberdyne and, therefore, no Skynet.
There is another theory is that it is not a paradox as such, more an alteration of the timeline and some clever writing by James Cameron. It is possible that, in 1984, the man who cancelled a date with Sarah Connor (a message on her answering machine) was indeed John Connor's "original" father. With Skynet sending the T-800 back in time, altering Sarah's traditional timeline, and in turn John sending Kyle Reese back in time; these events inadvertently altered John's birth father to become Kyle, rather than the unknown cancelled date. In effect, Sarah Connor would have become pregnant either way, "John" would have been born either way, and he still would have sent back Kyle (father or not). In Salvation
, Connor does not know about an alternate father, but for his own version of time to exist, he *must* send back Kyle. Skynet killing Kyle will help the Salvation 2018 timeline, but not eliminate John in any event. The same Cyberdyne didn't need the Terminator arm and the CPU, as it would have eventually come to be, without T-800 or Kyle being sent back.