Interesting problem.
I've only ever had one casualty in my skimmer, and that was in my old pond when I found the lifeless corpse of one of my yearling turtles in there. For what it's worth I don't think that turtle was in the best of health and likely would have perished anyway if left on his own in the wild. I read somewhere that in the wild the mortality rate of some species of turtles is about one in fifty that survive to breeding age, with the majority of them dying in their first year of life.
Maybe you just have to think of your skimmer as fulfilling the role of the wolf in nature that culls the slow, sick and stupid out of the herds to make for a stronger herd.
One thing I see though is it looks your skimmer may not have a basket? My skimmer has a basket that can't be bypassed by frogs or fish. Anything that gets sucked into the skimmer over 1/4" in size will get caught in the skimmer basket and can't get sucked through to the pump. Perhaps you simply just need a different skimmer design to stop the worst of the carnage.
Interestingly I have never found any fish, frogs or turtles, etc in my skimmer basket in my new pond, either alive or dead. I can't explain why, but perhaps it is because I'm only sucking somewhere between 1,000 to 1,200 gph through it compared to your 4,200 GPH?