The trailer didn't address that, but it would make a *great* plot twist. I kinda hope that is how it goes. Altho it's also possible that the "connection" between Smith and Neo allows Neo to control the machines in the real world, using some sort of link thru Smith to the OS running the Sentinals.
The trailer was just about Agent Smith wanting to take over the Matirx, and the Oracle saying something like she/they needed Neo to stop Smith.
I'm reading a lot of opinions on this movie, and one thing seems to stand out -- the talk between the Architect and Neo, at the end, was unintelligable to many many people who are not familiar with programming-speak. The architect spoke in "tech-ese" most of the time -- '"The One" is an anomoly in the system', and that kind of stuff. Many, many, many people who saw it have absolutely no idea what an "anomoly in a system" would be, or what that means. They don't know why that would make a system unstable, etc.
Many people didn't like it because they said it had no plot, and that there was too much "psychobabble". I believe it's because of that scene. It went over many people's heads.
I didn't think much about it at first, as it all made perfect sense to me (I am a systems architect). But the more I read other's opinions, the more I'm becoming convinced that is the case.