That was an incredibly depressing, but an incredibly brilliant episode. I admire any TV show that can pull off something like this, where there are no easy or right answers and where every choice sucks in its own way.
Having said that, I think that, despite Nikki's words, Gwen's interference ultimately was for the best. Nikki was spending all her time looking at video footage of crowds. Yes she had hope, but that hope had consumed her entire life, and it was all for nothing. In the end, she was getting rid of all that stuff, and finally moving on. Short term, this was disastrous, but long term, I think she's better off.
And this episode also gave us the flip side of what Gwen brings to Torchwood. Jack brought her in to add a human element. Sometimes, though, that's not enough. And Gwen has become so hard, as Andy said, that she needs Rhys to be for her what she herself is for the rest of Torchwood.
Jack's crap management style comes into play here. If he'd just been straight with Gwen or explained himself, a lot of this could've been avoided. (It would've been nice if someone, y'know, mentioned that Jonah spends 20 hours a day screaming.) Leaving aside any other considerations, whatever ability Jack had to just order the team around he himself abdicated when he disappeared to gallivant with the Doctor and Martha. Gwen was the one who led the team in his absence, and that means she deserved a helluva lot more than Jack shutting her down without explanation (and with lies, since his whole, "what can we do?" speech was done with the knowledge of that island).
Also: loved the byplay between Andy and Gwen, from her bitching at him for not attending the wedding all the way through to that last phone call. And Rhys bursting out laughing at Andy still carrying a torch for Gwen was just priceless.
Finally, what's all this about being surprised at things going into the rift? We've seen people do it several times, most recently Captain John in the season opener....