I'm not sure I ever would have bought it completely, but it was the clumsiness of the finale that really threw me as well. And I'll give the final word for now to Brett H., whose analysis qualifies as the most, shall we say, heartfelt. He explains, in part:
"The show at its core is about the need as human beings to integrate and sometimes supersede cold logic with a warm heart. That is the basis for the sexual tension between Booth and Bones as well as the foundation for the best relationships on the show. They have used Bones to show the positive, and yes messy, impact of moving in a heart direction. I think they wanted to show the negative impact of not being able to move in a heart direction. Zack was the character who couldn't connect at a heart level. He was dedicated to cold logic and saw little if any value in anything else, which made him capable of horrible things while being able to rationalize it."
If you read this blog much, you know I am very much with Brett H on this. He said it beautifully. I do wish the story line had been extended just a bit...but what's done is done!
The Evolution of Zack Addy
The Pain in the Heart Review
Matt Roush on the Finale