»Regarding Smith's contradictory comments...«

Smith remarks in Reloaded how Neo destroyed him yet he then adds how he was compelled to stay. How can he be compelled to stay when he is destroyed?

I don't think the program 'Smith' was destroyed, but 'Agent Smith' was....

In other words, he lost his 'Agent' job in the Matrix. You would think this would anger him, but Smith is actually a 'Free' man now, and knows how to bend the rules since part of Neo's code imprinted on to him.

Since Smith always had a hatred for the Matrix (primarily the PEOPLE and the SMELL of it), he took his anger out on the Matrix by cloning himself and destroying it.

So Smith chose to stay in the Matrix to destroy it, rather than fulfilling his karma and going to the Source to be deleted.