They absolutely worked backwards from their ending, or really a list of things they felt they had to have. Acccording to interviews with Orci and others it boiled down to: 1) Earth in jeporady because box office 2) Khan because Khan 3) Klingons 4) heavy focus on character development of Kirk. Nothing inherently wrong with any of those things but when you try to force them all together into a cohesive whole you get things like the Klingons being a threat you can forget about as soon as they show up, and Khan turning into a super bad guy because the plot requires him to be one. That in turn leads to very, very dubious choices like reprising Nimoy, who is always worth seeing but serves no purpose in what is almost certainly his last turn as Spock, and the reprise of the end of WOK.
They had a very promising and challenging movie in their hands. It deals with serious themes. Its reach exceeds its grasp ultimately. Using the Botany Bay as a point of divergence is a brilliant idea that doesn't require Khan. Harrison as a character, a super soldier experiment from the study of the B.B. is a great idea and Harrison doesn't have to be Khan. He also can be a more nuanced character, ala Magneto, then the maniac he ultimately becomes for the sake of some trailer bait. The silliness around is he/isn't he Khan diminishes him and the story. Him being Khan is pointless - Marcus (the real bad guy) takes him off ice to what design starships? Because Khan is the expert there? - and the obvious Federation response to the destruction of Vulcan by forgetting itself for a moment and creating super soldiers to defend against threats real and perceived goes out the window. Another missed opportunity is Marcus. He's ultimately a paper character. Why isn't this character Pike? He's the one who suffers directly in the first film, and would understandably respond the way Marcus does given the events that take place.