I'm not reading the new books, so tell me: does Superman react here as if he's never met anyone named "Zod" before? Because otherwise it'd be easy enough to keep the "Pocket Universe"/SuperKiller storyline valid. That tale involved a Zod of another dimension/reality, so retconning away all previous Zods from DC's "official" Krypton wouldn't have to affect him one way or the other, right? He came from a different Krypton in another reality anyway.
The only way Superman's killing of the other Zod doesn't count is if the currently-in-print Superman literally says something like, "Zod. What's a Zod? Never heard of him."
I went back to re-read
Action 846 to see how this is handled.
Wow. These guys are really good! It turns out you can read the dialogue either way, depending on whichever version of continuity you are assuming. Neither is contradicted and, impossible as it would seem, both are confirmed. This is from when Zod first goes public and attacks Superman - as they paste-up the street with each other, knock each other through buildings, etc, here's the discussion that takes place:
Zod: "Hello, Kal-El...
Superman... or should I call you
Clark Kent? We have obtained glimpses into your life on this primitive planet for decades, and yet I have
never understood your motives for self-degradation. Your father would be
disgraced to discover you
masquerading as one of these
sub-Kryptonians. You've embraced
their culture and abandoned your
own."
Supes: "
...GENERAL ZOD?"
Zod: "You
know of me Kal-El?"
Supes: "I've studied Krypton's history. You're wearing prison uniforms. You and your
friend are
criminals who were exiled to the
phantom zone."
Zod: "We are
not criminals. We are
rebels who had an opportunity to
save Krypton, but were denied because of the actions of
your father."
Superman: "I don't know how you
escaped, but as soon as I get a few hits in to remember me by -- I'm sending you
back."
Matt has shown that when he doesn't want to answer a question in his column, he can do a pretty good job of double-speak. But his answer to this question was pretty clear: In spite of the possibly ambiguous dialogue, this is the first and only Zod.