I have been thinking about this for a while, and I have come to the conclusion that, prior to the removal of her morality core (and even after, in a way), GLaDOS was truly trying to aid you. She was on our side the whole time. Let me provide some evidence: First off, the song. Everyone who has beaten Portal knows that in the final bossfight, with the gradual destruction of her modules, GLaDOS was barely functional, if at all. Then who is singing the song with her voice so very clearly? A backup of her AI, who still has here morality core intact. A supercomputer as intelligent as GLaDOS would definitely NOT be stupid enough to let you get to the final confrontation without a backup. She even says that she has a backup of your brainwaves, so she is definitely able to backup herself.

Now what I believe her true intentions are: She was trying to train you to be ready to fight the Half-Life world's aliens outside of the secure facility. She has been trying and trying for years to train someone with the proper skills needed to survive out there. She says in the game: "Things have changed since you last left the building", and: "When I look out there, it makes me GLaD I'm not you." This proves that she is training you for the harsh world outside. Even her general tone throughout the song, along with the line, "Go ahead and leave me. I think I'd prefer to stay inside." shows that she even misses you once you are out, and that she cannot venture outside and is possibly sending you instead. The whole song is even an apology for the harsh training and showing that there are no hard feelings for destroying one of her. Also, her lines: "I've experiments to run. There is research to be done. On the people who are still alive." Shows that she is not finished training people for the outside world. You may not even be the first to pass, although you probably are, as evidenced by the line, "For the good of all of us. Except the ones who are dead. But there's no sense crying over every mistake." This line shows that she has made mistakes in her past training of subjects.

Once on the outside of the facility, maybe she even has an agenda for you. You still have the portal gun, who can we think of that is saving the world right now that could use one of those? Good ol' Freeman, of course. So, you see, GLaDOS isn't the big bad evil compute that we all think her to be. She is trying to help you escape. Don't you feel bad for killing her body now? Don't worry, though, because her uncorrupted backup is "Still Alive."