Yes, she deserved it, because she was okay with helping rape Handmaids, kidnapping kids and purging people. And the spark of joy in the eyes of the enslaved women when they find the body says they were perfectly fine with Emily's actions. The fact that she was victimized by Gilead ( and she wasn't falsely accused, btw) doesn't make her innocent of everything else.
Most of the older Wives are Wives because their husbands created Gilead, which means they murdered more than one hundred million people. I like Serena, but she totally deserves to be shanked in prison.