Can we take a moment away from Agatha's all encompassing grief for her son and acknowledge Rio's grief as well? Because she's Nicky's mother too.
She is Death, her son was never going to live, and unlike Agatha, Rio had nothing to rage against.
She's the cycle of life and the inevitable end but does being the personification of that really change anything about the fact that she had to take the soul of her own son?
She gave Agatha the one gift that was in her power to grant - even though it was against her own nature and against the natural order of things - she gave her love time.
And Agatha had six years with Nicky.
She might have been able to watch him through every dying flower he plucked from its stem and she might have caught a few moments when Nicky was at his closest to her - likely whenever it had been a while since Agatha had killed the latest batch of witches and used their life force to extend Nicky's life for a little longer - when he slept and the delirium of someone terminally ill granted her access.
But those would have been stolen glimpses. Brief, and precious, and painful.
And Agatha could hate Death. Could take all that grief and turn it into anger. She could hide her pain behind that fury. There's a sort of relief to that.
Love so strong she broke the natural order that governs her? A son she could only love from a distance as he grew... but couldn't grow up? Eternal hatred of the one person in eons she had ever fallen in love with?
And maybe Rio can visit Nicky in whatever corner of eternity she had helped him cross over to - I hope she can, it would be far too cruel otherwise - but does that really erase the tragedy here?
And on top of that pain there's also the fact that Agatha has avoided Rio for centuries and ultimately asks Rio to promise her that she would never ever have to see Rio's face again.
Death can be cruel. But I think sometimes mortals win that particular game by a mile.