Unlike CO2, halon does not extinguish fires by displacing oxygen. Halon can be present in sufficient concentration to extinguish most fires without displacing so much oxygen as to prevent breathing.
I don't know the exact details, but halon takes advantage of the fact that most materials don't burn by oxidizing directly; instead, they go through several reactions in sequence. Halon blocks this process by combining with intermediate combustion products. According to the warnings I've seen on halon fire equipment, halon gas itself is non-toxic, but the gasses produced when halon combines with intermediate combustion products can be downright nasty.
All that being said, I don't think that a halon fire suppression system would have been much help on 9-11. A foam-based fire suppression system might have helped since--once sprayed--it would remain on top of the fuel and prevent re-ignition until the fuel was cleaned up. Halon, however, would most likely disperse before all possible re-ignition sources could be dealt with (given how hot the jet fuel burned, it would have quickly heated parts of the building well above the ignition point of jet fuel; unless those parts of the building cooled below the ignition point of jet fuel they would probably cause a re-ignition even if there weren't any other sparks or ignition sources still present).
Haylon works great for an enclosed fire with relatively low heat levels but would not work effectively on jet fuel. The other problem with haylon is that it is no longer manufactured. It's not ozone friendly.
A foam system would have helped, but it would have required massive amounts of foam to have controlled such a large fire that happened in an instant. In addition, any fire suppression system in place in the building would have been partially destroyed by the initial impact.
The design of the building gave thousands of people the time to get out. I doubt that any fire suppression system could have done more than slow the process down by more than a few minutes.