Can the imperial player place units on top of objectives such as terninals? Specifically placing a large unit in such a way as you are forced to kill it prior to bring able to activate it?

Yes.

You would still have to place the large figure in such a way that a rebel figure could not be adjacent to it (in order to activate it). Although you could still target a terminal for an attack because figures sharing a space with an object do not block line of sight to the object.

So lets say a nexus is on a terminal but you can be next to it, do you have to kill it to activate or can you ignore the nexus and activate it?

From what I understand of the rules, you could ignore the nexu and activate the terminal as long as the figure is adjacent to the terminal.