Henry Gilroy was on the Forcecast, a Star Wars podcast, that aired January 13 and confirmed there will NOT be a Season 2.
When asked by one of the hosts when we're going to see Season 2, he replied, "You're probably not going to because I don't know if you've watched Renegades and you saw the new trailer for GI Joe 2, it's basically the same plots. It seems the next incarnation of GI Joe animated is going to be probably have something to do with the movie."
It's at 58 minutes 54 seconds into the podcast.
ForceCast.net: Weekly ForceCast: January 13, 2012