Pops reprogrammed a younger version of himself and sent himself back in time to protect Sarah out of his love for her. But then you got me thinking...what if HE was the T-1000 that killed her parents??? Two things about her memory of the lake house that don't seem to add up:
1. That Pops could have killed a T-1000 then and there
and
2. He was sporting 1984 Gargoyles.
We know he couldn't have gotten the Gargoyles in 1973 because those glasses weren't out yet. He also couldn't have "taken them with him" because you can't wear glasses through the time field. But...if you're a T-1000 you can just make them appear on your face after you slaughter a nice couple at a secluded cabin. We know that Sarah didn't actually witness Pops arriving and destroying the robot because she was hiding under the dock. What if...either her parents were Terminators (which is probably too far "out there") or...Pops targeted them himself and murdered them not because he was on a mission to terminate Sarah Connor so that Skynet could win but that he killed them because he "loved" her and wanted to be her dad????
Now that'd be a pretty effing sinister take on Pops that I don't know that the filmmakers or Schwarzenegger himself would want to commit to. It also wouldn't explain why Pops was a true non-T-1000 T-800 in 1984. So there would still be some gaps to fill in. But it's just an idea, or at least 12% of an idea...