Alright, John Connor came to be because Kyle Reese was sent back to the past to protect Sarah Connor and ensure that John Connor would be born, which is an paradox in itself that I won’t get into.
Now, if John Connor sent back T800 in T2 and Cameron with the standing order of “Protect John Connor”, should they really be helping with destroying Skynet?
Because if Skynet doesn’t exist in the future, Kyle Reese need not travel back to the past, thus John Connor would not have existed in the first place.
So if their order is to “Protect John Connor”, wouldn’t they need to protect Skynet as well? As for Sarah, if she stops Skynet, doesn’t she sacrifice her son?