In a scene that was hard to watch, Harrison saw Dexter's entire ritual. Rather than being a romanticized version of Dexter the vigilante that makes him look like a superhero, they really highlighted the disturbing reality of what Dexter does, and how much Dexter gets off on it all -- which was very deliberate. He doesn't do this only to "save lives" and to keep his urges at bay. He kills people because he loves to. Everything Dexter said to Kurt about why he kills women -- he loves the hunt, the rituals, the feeling of power and control he has over his victims -- can be applied to Dexter himself and his victims. Setting up the kill room, showing and telling his victims what they've done, killing them, chopping up the bodies, all of the blood -- Dexter loves it. They even made a point of drawing a parallel between Dexter and Trinity when Harrison was freaking out. The code is just a tool Harry gave Dexter to evade capture and prevent him from killing innocent people, although we know several innocent people have either died, been hurt, or gone down dark paths (Deb and Harrison) directly or indirectly because of Dexter.
Harrison may have some dark urges of his own, but they don't seem to come close to Dexter's yet. I think Dexter made a mistake in showing Harrison everything about what he really is, because he was convinced Harrison is just like him when he's clearly not.
Right now, Harrison seems to be on board with all of this, but I'm not sure that will be the case by the end of the finale. Dexter doesn't even know it yet, but the walls are closing in on him. The first rule of the code is "don't get caught". This gives Dexter an "excuse" to kill an innocent person in order to evade capture. Once Angela either confronts or arrests Dexter about all the BHB stuff, he's going to be faced with a choice. He may even need to kill a cop or Angela herself in order to keep his secrets or escape custody or even to protect Harrison from being linked to this. If Harrison realizes Angela or Audrey's lives are in danger, or that Audrey may become orphaned again, he might realize that Dexter IS a threat to innocent lives and that Dexter himself fits the code.
After all, the only reason Molly is dead is because she was suspicious of Kurt and on to him, which all started once Kurt's son went missing. Dexter killing Kurt's son and toying with Kurt is also what almost got Harrison killed, which Dexter admitted.
I think there's a very good chance that Harrison turns on Dexter and either aids in Dexter getting captured or wounds/kills Dexter himself. It seems like this season has put almost all of the necessary pieces in place for something like this to happen. This would break the cycle of death and misery in Dexter's life and the lives of everyone close to him. It's also the only way for Harrison to be able to live anything close to a "normal" life.
They didn't spend precious time showing Harrison getting a long range rifle and being an amazing shot for no reason. Kurt's dead, so who else would be a threat or who would be most likely to need to be shot while running away?
Think about when LaGuerta died. Deb was faced with the same choice and she wrongly chose to kill LaGuerta over Dexter. I don't see the show repeating the same thing again. Dexter can't run away from this one.