I'm sorry you had that happen, and you did the right thing in separating your couple.
You should at least try to put one perch on your budgie's cage once he is less stressed. Also for future reference and for fairness reasons, it's always best to place the attacker bird on the spare cage and let the victim stay on the cage they are more familiar with. They shouldn't have to go through yet another potentially stressful event by being placed on a different cage.
In your case and since you have recently rescued these budgies it's very likely they haven't yet had the time to properly adjust to the new environment.
In order to make them both more comfortable, you can cover their cages on 3 sides and also have some background noise from the radio or TV for them.
I hope all goes well and it will be wise to keep them housed separately from now on.
RIP sweet Tito (Summer 2008 - January 17th 2013).
You are missed and never will be forgotten.