Part of the aggressive behavior may be due to having two queens , it would be almost like one hive robbing another but happening inside , if you had another excluder and super you could place the extra super and excluder under the top super to create a little gap between the queens and take some 1"x2" 's and make a spacer with a space cut out so bees can go in and out and place it between the top cover and super with the bee space just on top of the super ( I actually have a super with a hole drilled in at an upward angle that I use in the summer to alow extra air movent in a hive that is out in full sun or o. A hive that has several supers on top to give them a shortcut to the top ), if you do have two queens this will help sepperate them and help with the agretion plus with two colonies working together to fill the extra super it will go faster .
You could leave the colonies like that through the winter with the extra super between for food and split them early next year when they go into brood production , the smaller colony would have the warmth of the bigger colony below to help them and cutting some foam insulation into panels to help keep the cold out wouldn't hurt .
I had forgotten about doing that before with a colony that got knocked over ( horses) during a cold winter rain , lost a lot of worker bees but the queen and most of the brood was alright , I placed a screen over the hole in the iner cover and placed the weekend colony on top , the warm air from the lower colony helped save them , plus I took the honey they had and warmed it up in the house before putting it back in the hive .
Oh , and I have seen a couple of swarms get mean , they settled in a tree and a cool spring rain that lasted a few days kept them from moving on , they started their new home there and was getting low on the honey they took with them , they weren't to happy with me relocating them but they settled in nicely . My father did the clip the limb bit one time with bad results , back in 06 we had a drought and warm spring , the cedar limbs were brittle and while standing on a stepladder my dad tried to cut the limb the bees were on , he tried to use the shears with one hand and his shoulder , when he couldn't get the limb cut he reached up with his other hand and was going to get the cut started , well the limb snapped and about half the swarm ended up down inside the back of his shirt and the rest was in his face , hat and everywhere else , he ended up with close to twenty stings and feeling sick for two days ( slightly allergic to them now ) but we saved the swarm .
With close to fifteen years straight of keeping bees and a few years of helping my dad back in the eighties I have accumulated a few stories and knowlage on bees .
At one time we ( us three brothers and our father ) had close to 50 hives ( twenty were mine) , we have gotten smarter and have cut back to numbers we can handle and have a full time job also .
We try and stay chemical free in our hives and so far have had good results , we do loose a hive from time to time but everyone looses hives , kinda like building a bow , sometimes you break one .