According to the rules after a player activates the FTL Control location the fleet jumps immediately and the Jump preparation track is reset. After that occurs do they draw a Crisis card or is the turn done at that point? We have been playing that we still draw a crisis card but we are not sure if that is correct.

Yes, you still draw a Crisis card... nothing in the rules indicates that you should skip the Crisis part of the turn. The only time a Crisis card is not drawn on Human player's turn is if that player is in the Brig; even if a Cylon reveals on another player's turn, that player still draws a Crisis card and finishes his/her turn as normal.