It mattered when you were there near the buttons. The only ending, that goes in conflict with the sequel - Panchea's destruction. Unless Jensen survives somehow.
It's actually pretty cool how they got out of the situation. I think it's pretty realistic, given how our world is moving towards "opinion inflation". Everyone has an opinion, but the world keeps spinning. There are pro, neutral, anti-augment groups, and many of those, who want to play beliefs and convictions in their favor.
As for Malik, I actually didn't know she can be saved and just run to the elevator TWICE. I don't remember how I learned about that, but as soon as I did, I had to replay the game for the third time to save her. It was incredibly sad moment and she was my favorite supporting character in the game. And the game was really rich on awesome supporting characters.
P.S. GAWD, WHERE ARE THE NEWS ON DXMD???? The promo campaign will resume in June on E3?