I think there would be a lot more immediate and bigger reactions. The Omega attacking the beta would probably confirm some of the Beta's fears surrounding Omega's and Alpha's, and damage the relationships of everyone in the pack. The Omega would definitely know that the did something wrong, especially if he broke skin.
I think it probably go something like: the three of them discover that the Omega is infertile a little while after they discover the Beta is preganant. He goes of to grieve away from the Alpha and Beta. The Beta goes to comfort the Omega, and in his grief and self hatred he attacks her. The Alpha hears the Betas cries and runs to help and is able to get the Omega off with only a few scratches and bruises. There isn't much physical damage, but there is massive emotional and mental damage. The beta would probably run away to hide. She would be terrified of her own mates specifically the Omega, and it would take hours for the Alpha to cox her out of her hiding place. The Omega would ultimately end up hating himself even more and see himself as a danger to the Beta and baby. He would probably end up leaving for a while to allow the beta to feel more comfortable and less stress. The Alpha would be absolutely stressed about the situation. On one hand the Omega attack their preganant mate. She's terrified of them now and all the work they had put in to gain her trust has been lost. One the other hand the Omega is hurting and he ultimately didn't mean to hurt. The only thing he really can do is comfort the Beta, and wait for her signal on how to move forward.
They would need so much counseling.