In Man of Steel Kal-El asked Jor-El:
Why didn't you come with me?
His answer was:
...Your mother, Lara, and I were a product of the failures of our world as much as Zod was tied to its fate.
If they were genetically programmed, how could Jor El have a naturally born son? If he had no free will then how could he become heretic?
Assuming we stick exclusively to the 2013 "Man of Steel" film and its novelisation, then the answer to your question is that the genetic code of each newborn shapes their skills and abilities (teacher/scientist/leader/worker/etc) as well as determining their general outlook on society and their place in it.
Krypton had long ago abandoned the unpredictability of sexual reproduction—with its reckless pairings and random mixing of chromosomes—in favor of a more orderly and scientific system that allowed for complete control over each child’s genetic makeup and destiny. Nothing was left to chance. Each developing embryo was expressly designed to fulfill his or her preordained role in society—as a worker, warrior, thinker, administrator, or whatever best served the greater good.
The Genesis Chambers were the ultimate expression of Krypton’s rigid caste system, applying advanced genetic engineering to an inviolate tradition that stretched back to antiquity. Jor-El had sprouted from one such stem, many cycles ago, as had Lara, and Zod, and every Kryptonian who currently breathed upon the planet.
Save for one.
This doesn't mean that their actions are pre-determined though. It's a fundamental irony of the film that whilst Jor-El has gone from being a staunch supporter of the council to a "heretic" and Zod has gone from being a loyal General of Krypton to being shunned as a "terrorist", neither of them have actually changed their philosophical positions over the last few hundred years, just their methods.
Oh, and as to how Lara-El and Jor-El were able to conceive a child, I shall leave that to your imagination.
