Bear in mind that, by this point in the movie, Zod has already done all of the following:
- Killed Clark's biological father, Jor-El.
- Threatened/almost choked to death Clark's Earth-born mother, Martha "Ma" Kent.
- Shown Clark an apocalyptic vision of the future wherein the entire human race has been reduced to a pile of bones.
- Killed tens of thousands of people in Metropolis with the "world engine"/Kryptonian terraforming machine.
- Personally sworn to kill every single man, woman and child on Earth, one at a time (presumably while Clark watches helplessly), just to make Superman suffer.
With all that said, Zod - at this moment in the story - is literally inches away from killing a young couple and their daughter using his new-found heat vision.
Superman: "Don't do this! Stop - please!"
There is absolutely no other recourse, outside of killing Zod, to save these people's lives... but Clark hesitates. Wouldn't it be just as wrong, if not more so (killing, after all, should be against what Superman "stands" for), for Clark to take Zod's life?
In the end, Zod mows down the three innocent human beings.
Zod is subsequently incarcerated, and sentenced to live out the rest of his days in solitary (and allegedly escape-proof) confinement. And then, once he again inevitably breaks free from his imprisonment, he makes good on all his previous threats.
Look - I can understand being mad at the writers for placing Superman, as a character, in such an untenable predicament... but Clark absolutely did the right thing in this situation.
What other choice did he have?