First of all, be assured you will not have to return Connor to the shelter...just imagine what is going on with the cats right now:
Cats do not have a constant order like dogs, rather they have involved a certain place and time schedule also, that means if it is okay for Connor to be in a certain place in the morning it is not acceptable for him to be there in the afternoon.
Ally tries to show that she's the top cat, that's because she uses the same litter box like Connor, cats outside always mark on other cats' scent and feces to clearly show them, this is my place at this time!!!

I think the main problem is not aggression, but Connor's deafness...is it that he often doesn't react to Ally...she may get angry because of his non reaction and jumps on him and Connor is scared (who wouldn't at such a sudden attack!)...

Your cats seem to be alright after such a fight, and they even be together again without showing signs of fear or aggression...I think their problem is only related to reaction and non-reaction...
and I guess they are even more scared when suddenly the humans interfere and become nervous, too...

I think Ally has to learn that Connor is deaf and it's not him being mean, but it's just simply that he can't hear and Connor still has to learn Ally's complex rights at the house.
Just play a lot with them together and talk to them often, maybe then Ally gets a clue about Connors reactions.

Although a cat often doesn't calm down immediately after an attack, sometimes they are so excited that it takes quite a time until they've calmed down. Both cats seem not to understand each others cat's reactions, like:
"Hey Connor's in my place! Get out of there NOW!"
"Hey that guy doesn't listen!"
So Ally jumps on him and Connor being scared doesn't understand it at all and reacts with defence, wondering "Hey, what have I done???"

There are two very good books about it, I've recommened them here already a few times. Please, give it a try!!!
Is your cat crazy? by John Wright
and
The cat who cried for help by Nicholas Dodman

I know your cats will learn to understand each other!!!