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your first question.... my understanding is that Smith was VIRUS. A virus infects files/programs and such. Through Neo the computers where able to elminate the Virus from the matrix. What happens to a file or program you have when a virus has been removed? You are left with the file or program right? Once the virus was removed from the system, the matrix was restored.
To your second question, we saw just before that what was going on in the real world. The machines and humans had a truce. Then inside the system, we were shown the Architect and Oracle discuss the release of those that wanted to be freed so we were basically told humans would be freed.
I have to agree with Mikado that though there is a truce now between man and machine it will grow thin and the entire cycle will repeat itself bringing about another war and another savior.
History repeats itself...over and over and over and over.
Thats just my take on it.
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