If he did not...
...commit suicide why would the government wait until 2004 to kill him?
I liked the movie but, as others have posted, it did seem to wrap up pretty fast at the end. Unless he was working on a new investigative article in 2004, which the movie never mentioned at the end, there was no reason for the government to "Kill the Messenger" in 2004, seven years after he resigned from the San Jose Mercury News.