The link below expounds on the reasons in greater detail, but his incarceration primarily revolves around him ordering the destruction of the Nauvoo Expositor printing-press and for treason: http://en.wikipedia.org/wiki/Death_of_Joseph_Smith
Micah I shun you for citing Wikipedia as a source and breaking the rules of referencing 101. ;)
Shunning is a religous tool designed to keep members in line. I would also say that just because it is from Wikipedia doesn't mean it is wrong. I made the assumption or leap of faith that Micah had read the Wikipedia article and found it accurate and precise.
As for me I have a no shunning policy, even for those who reference Wikipedia :)
I found this article from Bill McKeever on the Mormonism Research Ministry to provide some answers to the OP's question.