And combined with Klingons who had been changed into even-more alien form, the ratings-dolts would consider it close to monster-killing - something they've always accepted. Also, ratings-boards give outer-space science fiction uncommonly harsh ratings. For one thing, some time back, influential theologians twisted religious text - humans must the the only intellegent life. That, and the tolerance, and imaginativness, and several other things about SciFi, offend ratings-morons. But ST VI was a very mainstream movie, and it was seen as slightly-campy, self-depricating nostalgia, so they eased up on it.
It all sounds goofy, but ratings boards are run by goofy folks.
Afterthought: It also had the overtly-obvious political message about the end of the Cold War, and our very reality-based worry that Gorbachev was assasinated at one point. We came out on the happy side of the Cold War, so it brought up pleasant thoughts. That's something that made Western rate-ers very happy, they couldn't help but like it.
So ST VI got the kind of violence rating that non-SciFi, or monster-kill movies get.