Although a vet check is worthwhile, it may not show up a chronic issue. We've had 3 very aggressive rabbits who screamed on handling. Rosie was perfectly understandable, was terrified after having cigarettes burnt onto her and was unbondable. We would handle her with padding and thick gloves, Mike doing the bulk of this, and by the time she died we were able to pick her up without protection.
Ziggy, as far as we know, had no reason to be aggressive and after regular handling was safe to handle, although he didn't enjoy it. He was bonded with Sorrell and although they were not cuddly they were happy with each other's company. I suspect it was something neurological with Ziggy as we found him collapsed one morning ( suspected fit) and he was dead on arrival at the vet.
Olga was one of the Aberdeen rescue buns, and given an emergency spay as we were told Domino had got into her cage 2 days before we picked her up. Unfortunately the vet nicked her small intestine during the op and she then reacted to the combi vaccine, showing slight signs of nodular myxo. I think she either associates handling with unpleasant treatment or she had a low level discomfort.
She is happily bonded with Domino and are very close, she is still aggressive on being picked up though.
I would suggest that even if given the all clear by the vet you try a short course of Metacam, if there is low level pain this should help her temper.
Personally I would not remove her from being beside Clarence, at least they have some company that way, and they can get used to each other. Slow bonding may be a better idea in this situation anyway.
If you feel it's too much, and I can understand it, it may be worth asking a sanctuary to help.
I don't know where you are based but Collielover in Fife specialises in aggressive buns.