As for the Marathon trademark, it could very well just be an update to an existing filing. The inclusion of references to several past Bungie logos in the Bungie Aerospace filing, however, suggests a possible rebranding of the studio -- something we wouldn't be particularly surprised with considering the break with Microsoft way back in 2007, not to mention the fact that this fall's Halo: Reach marks the last Halo game from the studio before Microsoft's 343 Studios fully absorbs the IP.
Oh, and no, Bungie won't be joining the Richard Garriotts and John Carmacks of the world in heading into outer space, as both trademark filings fall under the usual USPTO video game classification. A Bungie representative told Joystiq "No comment" when asked about the listings, but for now you're free to speculate along with us to your heart's content.
Source 1 - USPTO
Source 2 - USPTO