I simply see it as a different telling of the story, albeit without known motivation for that telling.
A different telling is the exact reason why it should be done this way. Its got to be tough to keep a character like Superman fresh.
Keep in mind that it is also not the first time the Kents have been dead, through multiple media.
Glenn Ford dying in the movie.
They died in the Golden Age, Not sure about silver (Matthew?) and Pa died briefly after the 86 reboot. Then Pa Kent
Bo Duke died on Smallville while Lana Lang Ma left for the Senate pretty much abandoning her 19 y/o son to take care of the farm and family business.
But we went through most of that with the character, sharing those moments with him. That is not the case in the new 52 revamp.
Which suggests the reasons for doing such were because the other options were stale.