Yeah, I liked the quote, "It's not what you are, it's what you do." It really sums up Sam's feelings about his own powers. But at the same time, we saw that even though the whatsit in this episode used his powers for good (saving his wife) it still turned him into a monster. It seems to me like a really obvious metaphor for what's happening to Sam.
I wouldn't be surprised if Sam keeps getting put into positions where he's forced to use his powers to keep him or Dean alive. No more sneaking out at night to exorcise demons, but more using the abilities in self defense, which Dean will probably have a hard time stopping (or justifying why he should stop it).
I have two theories about this:
[sblock]1) Ruby is part of Azazel's plan and she needs to teach Sam to use his powers so that he'll be ready to use them when the plan comes to fruition. Right now he's just "practicing" on demons, but later he'll be put into a position where he has to use his power against something else - like the angels - probably in self defense or in defense of Dean. When that something else happens he'll be so used to using his powers that it'll be instinct for him to lash out with them.
or
2) Everything is backwards. Ruby is truly a demon who's seeking redemption, so to speak, and is helping Sam because she wants fewer demons in the world and Castiel has a darker side. He wants to stop Sam because he really doesn't want Sam killing demons.
I think the first theory is more likely, but I'm so used to looking for twists that I wouldn't be surprised if the second is what happens.[/sblock]