Just like to mention that Smith does not delete the program that he inhabits, which is made clear at the end of the film for 2 reasons:
1. The oracle, Seraph and Sati (the little girl) are all fine
2. If Smith delelted programs when he took them over, he would effectivly kill all the people he took over as well, so he would have already killed off nearly all of the human race.
It is only because once the mind is separated from the body that humans would die when inahbited by Smith, but as programs need no tie to a physical world to survive, they will be fine once Smith is deleted.
Also, in reply to the agents dodging bullets at the start of the first film, you must remember that Agents rely on a world based on rules, which they can ony bend. Have you ever been sjy-diving? it is incredibly difficult to actually move from a fixed point in the air while you are not touching anything, so unless the agents can move their bodies in ways that joints can't move, then if an agent jumped through the window in the Trinity scene, he would have had a very hard time moving around in the air to dodge the bullets.