People are far more receptive to listening to someone they trust over someone they don't. It therefore follows that the mom was far more likely to have trusted/respected her son enough to hear what he had to say than the opposite. It's all the same assumption.

But sure, let's go with the alternative; she's a complete asshole who used religion as her crutch to do horrible things to her son all her life, and her son finally talked her into realising that she is the monster who has been causing issues this whole time. This is its own assumption too; we don't know what their relationship was like.

Her son, after showing her how horrible she has been her whole life, runs off to celebrate this victory with his friends, and leaves her to cry on the floor, alone.

He cared more about being right than anything else, including helping her through this discovery or damn, even just calling someone she trusts to talk her through it.

So the point of the comic stands regardless of this assumption. The son abandoned his mother after turning her worldview over completely. The consequence of that was his mother lying on the floor, devastated. (Whether she deserved it or not)

Does anyone really deserve that? Did you enjoy having to figure out what to do with yourself when you realised that it's entirely likely that nothing outside of this single life exists, all on your own? Would you have appreciated a friend or family member walking you through the way to handle that?

A little bit of empathy goes a long way.