I don't know, maybe I'm missing something, but it just seems crazy that people get so worked up over a 2"x1" square on a loading screen that no one pays attention to anyway.
Look, I'm not some marketing executive painfully trying to trumpet the virtues of in-game ads and their "benefits" to consumers. All I'm suggesting is that people keep it all in perspective and not attack something simply for being without considering the circumstances. There are in-game ads that are well-implemented, ads that are implemented awfully, and ads that are out of place but not really obnoxious. As far as I can tell, this is in the 3rd category. Yes, it's not exactly great, but its also not the end of the world. It's nothing that should keep one from playing a great game (if Deus Ex is a great game, I haven't played it). But then again, if your principles are that important to you, and you don't care about missing this game, then that's your own business.
Again, all I'm saying is, keep it in perspective.
P.S. Seriously, the Star Wars changes are not that bad.