1. If you're going to end Torchwood (the organization as well as the series), killing three-fifths of the team and making the leader leave Earth works.
2. Jack reneging on "An injury to one is an injury to all" is bitterly, bitterly unpopular. Unfortunately, Jack has had moments when he didn't exactly stick to this credo, so it's not completely out of character. It's damned unfair, and it really couldn't be crueler to have put him in the situation to make that particular sacrifice, but at least the writers recognized that that's really it for Jack. He can't stay here any longer after a decision like that. He's no longer our hero. He can't die, so at the least he has to leave Earth.
(Mind, I don't like that choice. It was a very mean thing to do, to take away the Jack-as-hero perception. I can't argue the structure of it, but I will argue that it sours the audience. An audience might grieve and that is the way of sad events in a story, but souring the audience is a risky choice.)
3. Watching the politicians of Earth turn into genocidal maniacs was brilliant, but I'm sorry, that demands an ending far more devastating for the majority of them. Not all of them could/would/should get Frobisher's ending, but we really needed to see more death/imprisonment/suicide/abject public stoning of these characters.
4. Similarly, when the world has gone stark staring genocidal you can't gloss over that with a "Six months later." I think the descent into hell that this miniseries depicted was fabulous but the world would be irreparably scarred if it could come back at all from a devastation like that. Children ripped from their parents' arms by their own government. Chaos and anarchy, guys. Riots in the streets. Not "Six months later."
You can hate the deaths, you can hate what they did to our Captain Jack Harkness, but as for me I'm vilifying them for dropping the ball on the resolution. Which is a serious pity, since most of it was tight and horrifying and brilliant. Bad writers, no denouement biscuit.