Darker than a Bog Invasion causing billions of deaths and almost wiping out every race inthe Alpha and Beta Quadrants?
Darker than political assasination to manipulate trends in a war?
Darker than genocide?
Darker than Section31?
99% of the time though, Trek major actors are always the morally upstanding people fighting the evil corrupt dark people. The one notable exception are Janeway trying to kill that ensign for information.
Even Sisko when he threatened to destroy the biosphere of a planet backed off and it's unclear if he would have gone through with it.
Trek characters are rarely if ever the darker figures. Times have changed, I agree with the OP - audiences demand more complex characters today than in the past.