Except that what happened here very blatantly does not reflect what happened in Nightwing. If they had moved the bodies to a secure location like they did in Nightwing, the bodies should not be here for Black Hand to find. Except that here they are. So either Johns did not read that issue of Nightwing, or he did and simply retconned it in order to write what he wants to write; to be honest, I'm not quite sure which one would be worse.
As for him working with Tomasi on Blackest Night...just because writers collaborate doesn't mean that they don't often contradict the other's works, especially if the work was not directly related to the current collaboration. And I've got a glorious bridge to sell if you think that Tomasi has nearly as much say as Johns in regards to what happens in Blackest Night. Apologies for the snark, but it is what it is.