In Terminator 3 we learn that the T-X had the ability to use nano-bots to reprogram and control machines and Terminators alike.
In Terminator Genisys a T1000 "drips" into the head of the deactivated young T-800, and it turns back on.
So why didn't he
or the nano-machine hybrid John Connor
just injected some nanomachines into Pop's head and reprogram it to help him to kill Sarah Connor?
Considering the conflicting canon of movies with A) time travel and B) Creator disputes, it's hard to tell.
In Terminator 3, the T-X can infect multiple things with borg nanomachines. Supposedly, it was specifically designed to do this as the Resistance was capable of reprogramming Terminators to use against Skynet. The T-X could reprogram the human designed T-1, as well as the Skynet produced T-850 (but it rebooted to undo the mind control... yea.)
The T-1000 in Terminator 2, did not have this capability, suggesting that the T-800 is one of the few human reprogrammed ones, and the T-1000 series was not designed with this possibility in mind. The T-1000 is also T-1000, advanced prototype. A mimetic poly-alloy. Liquid metal.. It is one of the first, and not a full production model.
Now Genisys, which frankly ignores everything in T3, uses the mimetic polyalloy to repair a disabled T-800 series Terminator. It doesn't explain how. Did it just reboot it? Did it fix circuits? Did it emulate circuits? Did it fix or become a new battery? They don't explain. If it could emulate circuits, then it can change how the circuits respond, and the programming.
As they mention in the film, mimetic polyalloy does nothing until programmed by a CPU. The T-1000's polyalloy is already programmed, and once programmed, it can be ordered to change shape, and it's default programming is to return to the main body when detached. The unprogrammed mimetic polyalloy at Genisys's headquarters was essentially programmed by Pop's cpu. As a blank slate polyalloy, it wouldn't reprogram Pops. It was still in prototype phase, and the infected John Conner didn't foresee using it to reprogram Pops. Arrogant bastard that he was.
So in the end, the all powerful Skynet simply didn't foresee reprogrammed Terminators as a problem to solve or a threat to respond to at the time, leading to the ability to reprogram them on the drawing board.
Firstly from memory it is the T1000 that drips some of its liquid metal into the downed T-800 to reactivate it, not John Conner, but the point is this:
The act of re-activating the T800 only makes it function again, there is no change to its programming. If John performed this on Pops he would maybe restore functioning, but the fundamental program to protect Sarah would still be in force. In fact the same method is used later on to re-instate Pops at the point the Cyberdyne facility is destroyed (as witnessed by Pop's "Upgrades" on saving Kyle and Sarah from the panic room).
