Thor fez não querer destruí-lo, eis porque ele fez isso:
1. Just after Vision is born, Steve asks Thor if he "Helped create this?". Thor replies with an affirmative tone that this had connections with the vision he saw in the Water of Sight.
2. When Thor is first enchanted by Scarlet Witch, he has a hallucination. In the Hallucination, Heimdall holds him, and then suddenly the screen turns white. Thor sees an image of the 6 infinity stones, & of Vision opening his eyes. This is the exact scene from the trailer, just displayed for a mere split second.
3. Thor & the rest of the team did not want the Infinity stone to touch the surface. This is confirmed when the Avengers are trying to get hold of the Cradle, & Steve tells them over the radio comm that "The stone should not touch the surface or it will wipe out the entire city". Thor could have shared the same fear, thus letting the Stone get integrated into Vision.