It's possible that Khan thought he would have time to go back for them after he got off Kronos. Especially if he thought Marcus was dead already. Though it doesn't seem like he thinks he's dead when he's in the Brig talking to Kirk, but maybe that was me reading more into it than I should
On the second note, there's actually a couple interesting points from the book that either got cut or just are used as explanation that sheds some light on the movie. Since the book got the writer's blessing, I'll take them - at least, for now - as canon, or at least as good possibilities.
1. Khan's lil tiny transporter that Scotty's carrying (and which was presumably in those duffle bags) wasn't actually a fully-functional transwarp transporter. The way it worked was that the mini transporter was custom built by Khan, and designed to relay him through a base on the moon with a minimal crew to a hidden ship, that THEN used all it's power to shuffle him off to Kronos, blowing it's warp core in the process. Which is why they couldn't just beam after him. It would take a looong time to replicate the entire process. It's still rediculous he transported all the way there, but that's more in keeping with Trek '09.
2. More important to this conversation - the whole scene with beaming the torpedoes is really detailed. So, apparently, the torpedoes WEREN'T armed. In fact, McCoy and Carol armed the one by accident. So I guess that points to the fact that Khan intended them to shoot them all at him and they'd just softland and do nothing (forgot about that in my previous post, sorry).
When Spock beamed them over, he activated ONE of them, taking the odds that Khan would have to scan them all one-by-one and would'nt scan that one in time to beam it off or know that anything was going down before it was too late. They all went off because the one blowing up blew the rest of their warheads.
There's also this long-winded story about how McCoy replicated biomatter and stuck them in the torpedoes so that with an initial scan they'd show as humans, but that just smacks of despiration to cover lazy writing in my book lol.