Your confusing what happened, with what his goals were. Sasuke's goal throughout the majority of the manga, was to kill Itachi, to do that he needed power from Oro. In no way was chidori'ing Naruto ever his goal, he was just in the way of his real goal. The Manga makes this clear.
He knew ever since the Uchiha Massacre about that, & it came up as a brief after thought while Naruto was lying unconscious. If he wanted MS. He would have finished the Job after hitting Naruto with Chidori when he got 3T sharingan. Like I said before, His goal was to get power from Oro. Refer back to this post, bringing scans. 2G data is a bit slow .