Well said, Jason.
The two of you are now adults. You are married, and you have a child together. You are experiencing adult situations and must react to them in an adult way. Ben, refusing to spend time with your wife because her parents make you uncomfortable is dealing with this situation in an immature manner. Crystal, accepting the things your mother says without protest and allowing her to dictate your life is dealing with this situation in an immature manner.
You have to make the switch to adulthood. You can't deal with adult situations like teenagers. Yes, Crystal, your mother will always be your mother; but Ben will also always be your husband. You have moved out of that phase of your life in which you are under the direction and rule of your parents. You and Ben must now grow together toward a future united as one. You cannot allow yourselves to be divided. What the both of you need to do is stand up for yourselves - your mother has no right to interfere in your marriage. The best that you can do is tell her that you are sorry that she does not understand your relationship with Ben, but remind her that your marriage is something sacred and that fact demands respect - holding on to bitterness is only going to poison your married life and the last thing your mother wants to do is cause you pain.
Stand up and tell her that that is what she is doing - she is hurting you. She is causing you pain. Why would you contiue to allow her to do that? Does she realise that she is hurting you?
You need to be the adults in this situation and tell her that she does not have to immediately think Ben is wonderful, but she
does have to love him - you, Ben, and Emily are a family now, and that is something holy and beautiful. Even though the situation in which that came about may be spurious, that does not give your mother the right to continue to punish you now for a poor judgement call that you made in the past.
But just as much as it is her duty to love both of you, it is also
your duty to love her, to pray for her, and to wish the best for her. Pray that her heart might be warmed and that her eyes might be opened. Do not return her bitterness and rudeness with anger and disrespect. Love casts out all of those negative things, and if you want this situation to turn around, the best thing to do is try your best to do nothing to merit her negativity. Refusing to spend time together means that she wins and feels justified in feeling like Ben is unworthy of her daughter.
Hopefully you can find a solution to this situation.