I just don't accept that the death of a parent is somehow an obligatory part of every fictional character's backstory. That's too formulaic. Superman got by in comics and TV just fine for over 20 years with both adoptive parents alive -- obviously it is possible to tell good Superman stories without orphaning him a second time. It. Is. Not. Required.
I don't really see it as formulaic at all. People lose their parents all the time; it's a part of normal human experience, so it only makes sense that eventually Clark would have to go through it as well. Not to mention that in most tellings, the Kents were already
up there in age when they discovered Clark, so the likelihood is even greater that it would happen before he left home.
Plus we're talking about the first superhero here. I think there have to be allowances for certain things seeming "formulaic", since a lot of them were originated with this character.