Shepard activates the Crucible, but it is the StarChild that allowed her to do so. Without the StarChild giving her those options, Shepard would not have been able to do anything. Without the StarChild, she wouldn't even have been able to get up there. In the end, the StarChild makes it all possible. He gives her a few choices. She cannot influence the choices, she can only make them.
If you have the choice to go either left or right, does that mean you have full control of where you go? No, as you cannot choose any other direction then left and right. The people (the StarChild) that made those paths (the choices) are the ones that control your path.
The Crucible does not require the Citadel/Catalyst to be fired, but it does require the Citadel and all of the Mass Relays to achieve what it was designed for; destroy Reapers across the entire galaxy.