Well it's hard to say. The big thing about Portal is that we don't know the full story and given the way Valve writes we may never learn it.
One of the reasons why the song "Still Alive" is so famous is because it acts as an epilogue to the game. Given some of the things GlaDOS says there, it makes you wonder how far gone she really was, and it makes it apparent that she is still conducting experiments and is apparently working towards some higher goal, perhaps "blowing a cog" having been intentional so to speak. Her actions both before and after the morality chip not seeming
all that differant since she tries to kill "you" even with it.
I'm sort of suspecting that everything, including the final battle, was part of that final experiment. GlaDOS is working for someone, presumably Apeture (perhaps remotely) and that cleansing the building and waiting however much time passed was all part of some greater plan. It's also hinted in the song that there are other experimental test subjects.
*THAT* said (I'm not a huge expert) I'd say that Black Mesa wins. Simply because Black Mesa generally does not kill their own people intentionally, which really, in the overall context of the story (including the "Still alive" song) seems to be what happened.
While it plays havoc with some revelations I was actually sort of wondering briefly if given the way the world looked in Portal if perhaps the whole bit with "we're releasing on time" might also imply that after the major catastrophe (invasion) Aperture/GlaDOS is trying to bring some of earth's best toys into play in retaliation. In the final equasion a very nasty device in the hands of what is now a very skilled user has made it into the outside world.
The point is that there are just so many ways you can read into it.
Your odds of living seem to be better with Black Mesa though.
>>>----Therumancer--->