I'll do what I've been doing for years now and ignore anything that is going on in Justice League or event comics. I don't care about that, much less when it's such a blatantly obvious cash grab like this (most of the people hinted to be dying in those covers had perfectly reasonable motives in their solo books for disappearing while the new generation took over, no need for this thing).
Really, PKJ will probably deal with this with a simple "oh, this story happens before those events" note, and by the time he catches up after Warworld and the multiversal arc he has planned, there'll have been another event comic to bring the old JL back to life. No harm done to Clark, or to the continuity of Action Comics. No need for this in Son of Kal-El, either, since Jon already was dealing with his father being gone.
But a lot of harm done to Diana (they just took out all the hype the audience might have had for the first WW-event in ages) and specially John Stewart (last time I checked he wasn't even in the JL, that was Hal, and now they bring him in just to kill him while Hal gets to be in the front and center of that cover). I hear the Stewart fans are already ripping this to shreds, and they should.