Star Trek's core identity is that its tone is "neither depressed, cynical or desperate." That's a pretty loose core identity which allows for a wide range of storytelling styles and topics.
Any franchise has to have some organizing principle - it can't just be "any bunch of people in a starship" - or else it has no meaningful identity, so what justifies using the same name other than crass business interests? Even McDonald's knows that when people walk through their doors, they expect to see burgers on the menu and not sushi.
Star Trek can depict dire and horrifying situations. But the attitude of Our Heroes must always stay within a basically positive zone, and become an angst-ridden navel-gazing self-flagellating wallow, a la nu
BSG. That seems like an eminently fair compromise between hanging onto an identity and allowing for plenty of artistic latitude.