The situation is rather serious and dire and full of ickness, but the ending and Jack's smittenness makes me happy inside. Is that wrong of me? Or have I just gotten used to Torchwood's brand of dubious conset ala aliens?

Possibly both. I ♥ the team joining forces to get UNIT Boy freed for Jack. I adore mention of Tosh's being freed and how it's exactly the same with Ianto; let UNIT think what they want, Tosh is brilliant and Ianto is too, and they're where they want to be.