If there's any explanation at all for not beaming up Kirk that has an ounce of credibility, I'd say it was Khan's growing increasingly irrational as the movie goes on. Hell, he didn't even really strand him. How could he even think he did? Kirk wasn't missing. Everyone knew where he was. He was beamed there from the Enterprise, for crying out loud.
No. He was beamed to Regula One with McCoy and Saavik. Nobody on the Enterprise knew about the underground base on the planetoid. Spock, Bones, and Kirk saw the tape, yes, but it was Kirk alone who put two-and-two together when they were in the transporter room.
So, If Khan destroys The Enterprise (remember, they haven't gotten out of jamming range by this point, so Starfleet has no freaking idea what's going on) nobody will know that Kirk is alive, or even where to look for him. Genesis was a civilian project. All the information about it was on Regula One.
I get the point being made here people. All Star Trek movies have plot holes, even the best, but that scene with Khan is not one of them.