I understand why your mom reacted that way.
she is scared that she wont get to spend an eternity in heaven with you. For a christian mom this is prolly one of the worst feelings they can experience. She is so scared, that she is trying to think of ways that this could have happened. She doesnt want it to be because "you" decided to be an atheist, so she is thinking of a way that would make it "reversible" or make it not your "fault".
when she told you that atheist were scum bags, she was trying to convince you not to be one. She is scared and emotional so this is really the only thing she can come up with atm. Thats why it sounds so stupid.
whe she told you that you are going through a stage, it was an attempt to make herself feel better. A way to reasure her that her little boy isnt going to go to hell. She is so emotional that she cant comprehend the fact that you would go to hell.
What I suggest doing is reconsider your desicion to be an atheist. I know that it may not be what you want. But its what I advise. But if you refuse to come to faith, then I suggest becoming closer to your mom. Im nota master when I comes to women, but try to do more things with her. Try taking her places and spending lots of time with her. This will make her feel better and help with your relationship. Its certainly better than distancing yourself from her.