I'm sorry that this happened to you. I've never accidentally killed a shiny as far as I can recall. I think I've captured every shiny I encountered in the wild, and all of the others I get from hatching eggs.
The closest thing to this disappointment that I've felt was when I was breeding Porygon with a Japanese Ditto in Pokemon Black (or White, I don't remember). I needed a Tepig for some reason (I think a friend needed it?) so I took the Porygon out of the Day Care and put the Tepig in. I got a Tepig egg, put the Porygon back in the Day Care, and rode off to hatch the egg. The Tepig that hatched was shiny and Modest, which is a horrible nature for an Emboar.
While now I'm happy to have a shiny Emboar, and I'm sure it probably doesn't necessarily mean my next Porygon would have been shiny, I can't help but feel that if I just waited to breed that Tepig then I would have hatched a Porygon on the next egg.
It ended fine though, because I continued the hunt a few months later and finally acquired the shiny Porygon I wanted.