It is true that for all teams go on about equal treatment, that only applies so far. Yes, it's important to give them an equal shot at beating the other, but if one eventually is obviously more likely to win, yo have to throw your weight behind them. Part of the McLaren Meltdown (Speaking of which, I'm going to Blog an in-depth analysis of that) was manifested in 2007 by their refusal to back one driver. Look what it got them*.
That being said, it's too early to think Brawn are favourng Jenson. If that does happen, it would come around Race 9 or 10.
*Also note they subsequently switched to a 1-2 System and immediately won.
As the topic starter I feel like summing up my opinion... you're right, the 1-2 system is the most beneficial for teams, it's been proven loads of timesin F1 history. However I hate teams who like to tell they're true sportsmen and treat their drivers equally when they don't. Things like these would ideally be best when clear from the start, otherwise they'll just add up to the bitter feeling you'll get when they come out afterwards. In the meanwhile I heard on the news Button saying he needs to win, and Barrichello hinting that he'll not accept another fake 'equal treatment' . (
http://www.forumula1.net/2009/f1/f1-news/rubens-to-quit-if-brawn-favour-button/)
Then, again, I think you're right, favoring one driver over the other is the most logical thing to do at this point: the team may need those points if the other teams catch up in developmant. Only, if they fake an equal treatment they lack sportmanship, sadly. Hope this won't be the case, It'd half kill the excitement of the next races and I actually really like both Brawn Gp and the two drivers. (...and sorry for this longish post

)
I'd love to see 'em race twice in tracks like Spa. Second time there could be in reverse for all I care. Bring in Watkins Glen, Kyalami, Imola, keep Silverstone... and reduce those start-stop boring tracks! Asking too much, yeah.