Definitely obedience, you are correct. I was thinking it might have been conscience of the guy himself. Well, it is what it is. Eleven can be a bit manipulative if he wants, and all bets were off when they started messing with people under his protection. (I figure also, "Under my protection" rather stood for the entire planet, and not just Clara)

I don't know who the woman in the shop was. River is the forerunner, I suppose. But it would be interesting if it's someone we haven't met yet too.

I wouldn't have gotten it from just Richard E Grant, but Ms. Kizlet actually does call him "Great Intelligence" at one point, which was how I got it. It was a very quick reference though.

Victorian Clara was less guarded, and she also just seemed happier with her life.

I think we don't know enough about modern Clara yet. I mean, she's happy enough with her life to not immediately decide to run off with the Doctor. It's like, to me, she knows that she doesn't need the magical man in the "snog-box" in order to go traveling. She'll still do it one day, and on her own terms. So he has to convince her. I didn't feel like she was as aimless as Rose, for example, or staying because of some mistaken idea of what her commitments were. She seemed more sure of herself than that, more mature even though she still is very young.