The actual bonding process itself is easier, because establishing a hierarchy between two is easier than three because the hierarchy gets more complex the more rabbits you add in. But that doesn't mean a pair is any more happy together than a trio - in fact, eventually if I have the money, I'll be getting another pair of buns to make a quad to make my current pair happier. It depends on the bunnies as to how they are happiest. The only reason people tend to have pairs is because they are the minimum to have and the bonding process is easier. It can also be tricky adding in another rabbit to a long-standing pair, as the original pair may split, so if people have a pair they often don't want to take that risk unless there is a particular reason for having a trio.
Please do not go swapping the buns around at all - now you have taken the dominant male out you will have broken the bond between him and the others. If you wanted to put them back together you would have to bond them properly now - I won't confuse you with going into the detail because I'm sure you're having to take in enough new info at the moment, but it basically requires a neutral space and constant supervision and needs careful planning.
To be honest, I would suspect that the males are not neutered, because their behaviour would only be normal for neutered rabbits if they have just been put together or were having bad problems in the bond, but then I would expect other bonding behaviour too, such as presenting to groom and chasing. Sometimes the female just doesn't get pregnant for some reason or she does and kills her babies when she gives birth. But wait to see what the vet says before you make any decisions. I'd also get the vet to give them a general health check whilst you are there, make sure they are a good weight and don't have injuries or sore genitals from all the humping. If they are not neutered then get the vet to check if the doe is pregnant (although they will only be able to tell if she is fairly far along) and discuss an emergency spay.
Don't worry, even if they are all unneutered, there is the simple solution of neutering them. It will all work out fine, so try not to worry.
