Can a F-4 Phantom II pilot control weapons?
Can the pilot in the front seat control the weaponry as well, or do they only fly the aircraft?


Yes, the pilot in the front could control all weapons. 


  And can the weapons officer in the back fly in emergencies, like, pilot is unconscious or something?


This is more complicated. The USAF F-4's did not have controls for the RIO's (now called WSO's), but the Navy/Marine F-4's did.