You have to question the sanity of anyone that thinks the safest place to keep anyone is in a torpedo
The plot of the whole film is pretty ridiculous. It's credit to Abrams that he managed to make it watchable. Hopefully they'll get some proper writers in for the next one though
Meh. It can be explained away. We don't know what his pristine plan was before Kirk got involved. He had to believe those missiles were meant for the Vengeance. He was proabably plotting to take the ship for himself.
Smuggling his friends aboard in topedoes with their warheads intact but unarmed like they were Trojan horses would be the the last thing anyone would think (it is a bit insane, after all), but if he gets on board and revives them, there's no doubt they'd take the ship over, and Khan would be on a rampage with the Federation's newest warship and 72 powerful missiles at his disposal.
As much as I liked this movie, it would help explain to the average viewer exactly whats going on. Something to the effect of Kahn saying to Kirk how he disrupted his original plan and then heavily imply that he was planning on capturing the Vengence when it arrived on Kronos to kill him.