Trek's never been so dark or brutal as to merit an R rating. An attempt to do so now would just make it seem like superficial pandering.
(Come to think of it, that's one thing I like about the Dominion War. As dark and terrible and heart sinking as it was, our heroes never really lost hope deep in their core. They persevered against impossible odds and won. That's classic Trek right there)
And the last sex scene in Trek involved Riker, Troi, and Shinzon. As far as I'm concerned, that's proof that Trek should never ever have another sex scene ever. Hey, I like them as much as the next hormonally-driven guy, but Trek ain't it.