As a former English instructor who once taught a course on children's lit...
My theory about the dead parent syndrome is that good parents usually limit the choices a child can make. To make for more conflict, more potential for interesting developments in the plot, the parents--especially the nurturing mother--need to be eliminated from the story.
The other options are to offer a "bad parent," e.g. the wicked stepmother, or to have relatively unrealistic scenarios for the child (that can still be entertaining!), e.g. Encyclopedia Brown, who had 2 healthy parents, but also ran a detective agency.
Don't take it too personally.

It is a common trope, but it's just a way to provide a child with freedom to make unusual choices. Pippi Longstocking is a GREAT example of this! Maybe if you explain it to her this way it would be less troubling to her?