As the myth goes, Kronos swallowed this children as they were presented to him, so he could prevent the prophecy. But why couldn't he kill them?
Cronus's children were gods, and therefore immortal. Until the "Pan is dead" tale, which was only related in the first century AD, no death of a deity is related in Greek mythology. Gods and Titans alike may be imprisoned or transformed, but not killed. This is unlike some other mythologies: whereas Osiris, Tammuz, or Baldur are clearly described as dead, the Greek equivalent, Persephone, is merely kidnapped by Hades.
In the story of Chiron, the immortal centaur, he is mortally wounded and wishes to die, but death does not come to the immortal. Chiron is described in myth as giving his immortality away to Prometheus, in order to die; even then he does not truly die, but is transformed into a constellation.
From this account it may be inferred that the Hellenes took immortality literally: not just unaging, but actual unkillability. This is supported by the myth of Tithonus, where it is apparent that agelessness and immortality were distinct concepts to the Greek mind: the former not being subject to growing old, the latter not being subject to death.
Thus, in answer to the question: Cronus did not kill his divine offspring because he could not---they were immortal, in the sense of unkillable. The most he could do was imprison them. Likewise, the gods later imprisoned Typhon and the defeated Titans, but did not kill them instead---not for want of will, but because even they could not kill immortals.