Add to this that Khan thought he was stranding Kirk in the center of a dead planet. Emphasis on dead. He hadn't been to the Genesis Cave. Khan's men never got any further than the station. He didn't know there was a natural paradise waiting for Kirk's landing party. He'd have been as amazed as Kirk was at what they found there.
But if he scanned the planet to locate the Genesis Device, wouldn't he have noticed all the flora down inside a dead world? Any other time, sensors can locate a pimple on an ant's ass but here completely miss a giant cave full of plant life and water?
It really is no more complicated than they wrote themselves into a corner so they changed Khan's motivation. It works because Shatner and Montalban chew enough scenery that you get lost in the performances.