It's interesting how they went out of their way to say her soul was destroyed. That's a worse fate than any other character has faced as she doesn't even get a nice afterlife. I don't know why they threw that in, unless they thought it was the only way the heroes would ever start giving up. Or, they're planning on some surprise opportunity later. The only other explanation is that they wanted the shock value.
I think it's just that, since resurrection had been established as something that could be done by a variety of means in the Buffyverse, and since several lead characters had already been brought back from the dead or had their souls restored to their bodies, the idea of death had lost its weight by that point. If it hadn't been established that Fred's soul was gone, then the characters and the audience would've seen Fred's death as merely an inconvenience, a temporary problem to be solved. And that's not what the writers wanted. They wanted a main-character death that had permanence and emotional weight, like it should. So they had to rule out resurrection as a possibility. They did the same thing with Joyce on Buffy -- establishing that natural, non-magical deaths were part of the normal order of life and couldn't safely be reversed. That's not about "shock value" -- it's about allowing death to carry its proper dramatic impact and meaning in a universe that's eroded those things through the overuse of the resurrection trope.