If I (playing the empire) place a leader into a system to oppose a rebel mission, after that is resolved can I then use that same leader to move troops into that system?

No. Placing a leader on the board is a permanent action for that round (except in the case of a few cards that allow you to move them for some reason).

It's part of the strategic nature of the game. During the planning phase, you need to assign leaders to missions. The ones you leave in the leader pool can be used to either move units, or oppose enemy missions. You need to decide what units you need to move, what missions need to be completed, and predict what missions the enemy may play that you want to oppose.