When I saw it was the Atom (possibly) I flipped. Good guys always going bad. Makes you wonder. Well, not wonder really, but the cliche becomes tiresome. Never so much as like a villain becoming good. That becomes a tad bit more interesting. Hank of Hawk and Dove, Obsidian, Parallax, Nuklon, and the Atom. Whatever.
Making him a villain is interesting, but a killer? Let's address this from the standpoint of a writer. The story has been rather well-written, because it points out most of the emotions and strains people would face in these certain situations (grief, denial, need for revenge, nostalgia). Being well-written, it has to explain WHY Ray Palmer would reduce himself to actually KILLING Sue Dibney. I mean, the evidence is there, and so is the motive (small footprints in her brain, getting back with his wife through reconciliation).
He is one of the smartest JLA members, and he could have made several deductions (capable-wise), like what would happen, and finding a necessary culprit/patsy for the crime (Captain Boomerang).
But it goes back to the whole thing of being cold-blooded. Who would have three people killed just to get back with his wife (plus having his ex-wife hanged, and Lois shot?--Sorry, I read ahead).
Plus, I go back to what Hal/Spectre said. If Brad's writing is as good and meticulous as he aspires to be, then Hal would have left a contributing detail by telling Ollie to get them and make sure they pay. That's plural, folks.
So, even if those footprints are Ray Palmer's, I believe there is considerably more left to this story than simply chasing him down through phonelines. A last-second confession? I don't know. Again, Lois still has to be shot (by who?), Bruce, Diana, and Clark have to stop liking each other, and some other parties have to be revealed. I think a lot of this comes down to Bruce.
Maybe the Atom was already a villain, and Bruce changed it around to put him in the league. Keep your friends close, and your enemies closer.
I was kind of thinking Mr. Mind was involved. I am clueless. "That's right, now stomp REALLY hard."
