Good call there. It seemed a little odd that she'd go quietly to a meeting that she knew would result in her own death, but I assume that's why they had all the talk about how she's the gateway to Skye's future. Apparently dead Raina had to happen, and she saw that and let it play out.
Yep, they did this one up right, though I was mildly disappointed that no one else of consequence died. (Well, presuming Simmons isn't dead, and that's next season's plot anyway.) Especially that Ward still lived. Was really hoping May would get her chance to put him down and we could get rid of him. Oh well, maybe as the new Hydra big bad he'll be interesting.
Plenty of injuries, though. Dearming Coulson was a surprise, because when he caught that crystal I was thinking "oh he'll be fine since he has that Kree blood in him". Whoops, not so much, good thing there's a big guy with an axe handy...
I really like what they did with Cal, although I wasn't horribly impressed with the Hyde version of him. Thought they'd juice him up more. The whole resolution of that little dysfunctional family was very well done, though.
Very cool bit at the end with the crystal->seawater->fish->your local grocery sequence. I assume they'll have some sort of technobabble next season to explain how it was diluted just enough to keep people from turning to rock from the inside, but still trigger occasional power changes.