It seems to me that the essential conflict here, if you ignore all the "racists vs SJWs" rhetoric, is this:
Some people think science fiction should be primarily about action, inventing amazing new gadgets, and people fighting aliens in space. This is called "hard" SF.
Some people think science fiction (or fantasy) should be more about telling stories that allow the exploration of real-world issues in a world whose cultures, asumptions, and in some cases even the laws of physics or magic, are constructed to throw them into sharp relief. This is called "soft" SF.
While there's some overlap - a notable example being the new Battlestar Galactica show - most authors fall primarily into one or the other camp. So having one set of awards for two genres, many of whose fans on both sides consider them opposed, is like trying to support a one-state solution in Israel / Palestine instead of a two-state solution: naïve.
This is analogous to how some tabletop gamers prefer RPGs that are "crunchy" with a lot of combat and mechanics, and others prefer rules-light systems that tend to gloss over the mechanics a bit. Neither style is "wrong" or "bad", they just may not be be compatible with each other.
I'm not sure whether separate awards for hard SF are the solution, or just separate categories (or a "hard" and "soft" winner in each existing category, maybe). But that's how I see this playing out in an ideal world.