I have nothing against them showing Sue have a sick sister and a soft side she will never show at school. It was some great characterization.
However, I do agree that having her not only feel sorry for Glee club in the season finale (which worked) but SAVE them, and not only save them, but TELL WILL and then compliment him as a good teacher?!?!
I mean it was a great scene, but now a lot of the tension between those two is gone. Because we saw when push came to shove she likes/respects Will and doesn't want to destroy the Glee Club really. That is a fine resolution for the end of a show, but now we know her sniping in future seasons will be just a lot of hot air. I think they revealed a little too much there. I also think having Finn and Rachel get together in the finale was a mistake because now we are back to a love triangle that was clearly resolved last season.
They'll just have to be more creative for plots, but the stuff that makes people watch (the vicious meta-sense of humor, Sue's verbal tirades, and usually great musical numbers) will always keep the show afloat.