I'm not going to claim she didn't plan to murder him, but the way the scene was framed made it seem (this is obviously subjective) like she was not 100% set on it until he said that SHIELD would be Indexing her people. At that, she brushed aside the peace offering and whipped out the crystal.
As for murdering him at all, I can't say it was right, but I will say that it was rational given what she'd seen. To her, war was inevitable, so she decided to make sure her people had the advantage. Also, I can't say that she was wrong, given that newSHIELD did want to bomb the place the second they found it.
But yeah, totally Inhumans Magneto, which would make Skye Inhumans Scarlet Witch/Quicksilver, I guess? Either way, it'll be interesting to see how everything shakes out next week.