Actually Smith has become more Virus like since the end of M1. He is still programmed to get into Zion, and he is still programmed to kill those who hack into the matrix, but, instead of being a regular executable program with a logical flow-chart like process, he is now a corrupted program stuck in a never ending loop that sees anything as an advisary if it is in his way of achieving what his orriginal program is for. That means even the machines themselves would be his advisary if he was not able to get into Zion's Mainframe because of them.
The simple answer to your question is, yes, taking over Bane is part of his programming because he is to do whatever is necessary to achieve the goal of destroying Zion. With the new abilities to copy himself, he used that as a tool to get into Zion.
In M1, one of the orphans at the Oracle's and Neo had an interaction with common ground being the spoon. The scene happens like this: Kid is talking with one of the orphans, who asks him to give Neo something. Though we do not see this, Kid says "Sorry sir, one of the orphanes made me promis to get this to Neo before he left" (or something very close to that), so Kid did not know about the spoon, but one of the orphans from M1 (who was released in the 6 months between M1 and Reloaded) asked him to do this favor.