I think that's part of why I prefer the continuities where both Jonathan and Martha are alive and well and an active part of Superman's adult life (as seen in the comics from 1986-2008, the '88 animated series, Lois and Clark, Superman: TAS
, and several of the DVD movies). Superman's story may have begun with a tragedy, but it's a story of hope arising from the ashes of tragedy. Having him endure the loss of his adoptive father as well (or both father and mother, in the pre-1986 comics) feels like overkill.
And what annoys me is how this trend seems to have cropped up in recent years that just because Donner's movie had Jonathan (and not Martha) dying, that means everyone has to copy it. We've had Jonathan die in Smallville
, in the comics in 2008, and now in Man of Steel
. Jonathan dying and Martha living used to be the exception to the pattern, something that only one version of the story had ever done. But because that version was a blockbuster movie, it seems to have overshadowed all the rest and come to be seen as the default.