I liked the movie up to the point where Zod's neck was snapped. I did feel a little sick seeing that. As the movie had pointed out several times, Superman is a symbol of hope and an ideal; he's smart enough and clever enough to find another way. What happened in essence is that Zod explained to Superman that a never ending battle with Zod would be hopeless; and Superman agreed.
Of course, the comics dealt with this also in John Byrne's Superman #22
...faced with a difficult decision of what to do with three depowered evil Kryptonians who committed genocide on a global scale, (Superman) chooses to execute them by fatal exposure to Green Kryptonite, watching sadly as all three of them fall.
That storyline led to a Superman consumed with guilt from this act; and he ended exiling himself into deep space so that he could try to cause no more harm in his solitude. Eventually Superman found redemption along with a piece of Kryptonian tech called the Eradicator
In the distant past, a dying alien race creates a number of containment devices in which to preserve their culture. They send them into space with contact teams, intent on meeting other civilizations. When a small group of these aliens arrive on the planet Krypton, they are met by the militant Kem-L, who kills them and corrupts one of the devices. Its new mission is to preserve his ideal of Kryptonian culture by eradicating all others — and thus the device becomes known as the "Eradicator."
On Krypton, the Eradicator does all that it could over the years to protect Kryptonians, even from themselves. When a group of Kryptonian explorers leave Krypton in search of a new planet to colonize, the Eradicator alters their birthing matrices and makes them fatally allergic to lead, thus creating Daxamites. To further ensure that nobody left Krypton, the Eradicator alters Kryptonians by encoding in them a genetic defect so that they will instantly perish if they leave their world.
It is interesting how nicely that folds into concepts introduced in Man of Steel; and Superman The Animated Series already took the step of combining the Eradicator and Brainiac.
Maybe Goyer and Snyder have a grand plan, and Superman killing Zod is the start of it just as it started a saga in the comics. We'll see. But I still felt sick watching Superman kill.