I think they were trying to sell the story of the referring giving Sting multiple warnings before pulling the trigger, so they could say he was so far removed from his principals that he didn't pull back when he had the chance. The problem with the way they did it though is everything you mentioned. Even if they let all those things go, Sting should have been DQ'ed for putting Abyss through the barbed wire, not shoving the ref. So at least you wouldn't say "he got away with all that other stuff, but they nail him for this!"
No one ever gets DQed for hitting someone with a chair OUTSIDE of the ring. Inside the ring, you'll see a DQ, most of the time. So if you are ok with the logic of the tacks just happening to be where he got chokeslammed, then you could logically say that Abyss just happened to have been upside down when he got hit with a chair. Pretty much anything goes outside of the ring, but once you're inside the ropes, you better play by the rules. Yea, it's pretty silly, but hey...that's the way wrestling works. Now touching or shoving the ref can, as we saw on Genesis, get you DQed. The wrestler is never supposed to touch or push the ref. The ref can let it go for a while, but after repeated occurrences, he has to take control and lay down the law. Yea, it's not the best way to end a PPV match, but if you go to the basics of wrestling, what happened can be logically argued.