I'd say that choosing a skill power (or a theme power, likewise) takes up both "slots" for that level, since it's not a wizard power. So he shouldn't get a spell and a skill power in the first place.
I'm not sure if that's RAW, though. I know a lot of the hybrid options are very clear about "only powers specific to the class benefit from this thing," but I'm not sure they clarified how the spellbook feature for wizards interacts with power-swapping for non-wizard utility powers.
(To clarify, I'm not saying that you are dealing with a hybrid situation, just that the hybrid rules are an example of a place where they were very careful to limit certain class features to working only with class-specific powers. I don't know if they did that, specifically, for the standard wizard's spellbook feature and non-wizard powers, though it makes sense to me that they would. It doesn't make much sense for a wizard-MC-fighter to get two exploits "for his spellbook" at certain levels. This may fall into the "knocking an ooze prone" area of "It works because that keeps things simple, figure out what it looks like at your table," though.)
Deadstop