I see what you're saying, but to be frank, I get incredible personal comfort from reconciling them.
And yes, it's apparently two seconds of the movie, matters not to anything, and it's even ambiguous at that. So, blame Pegg for "clarifying" it.
The problem is the importance and scope of the story is getting blown out of proportion. To that end, I regret the "two Sulus solution" in the real world because it lends credence (on the surface at least -- Quantum mumbo jumbo aside) to the idea that being gay is a choice, which is often the rationale for not granting gay people the same rights as non-gay people, and tends to go against the beliefs of most science. If this is the Sulu born before the Kelvin incident, then he's physiologically the same Sulu as Sulu in the Prime Universe. Of course, Pegg says that doesn't have to be now, at least I guess that's what he's saying. One Sulu must've carried the gene (or whatever) and the other didn't, I guess that's how he's rationalized it. He's essentially changed the Trek laws of physics once again. This time to placate Takei.
Anyway, this all went far deeper than Pegg probably ever intended. It's even got more legs and causing more buzz than blue warp nacelles did.
As a courtesy, he should've probably called Takei to see if he was OK with it before going ahead and "honoring" his character that way. Once again, we see what happens when we assume.