While the favouritism existed, I think people are making too much of it. I was watching a replay of the Istanbul incident the other day, and it hit me - it wasn't really anybody's fault. Given the position of the cars relative to one another, Mark Webber could see a lot more of Sebastian Vettel than Vettel could see of Webber at the time of the crash. It was a bit like Petrov and Hulkenberg colliding on the grid in Japan; if you have to assign blame, then one person might be more responsible than the other, but that doesn't mean the other person is exonerated. In that sense, I think Helmut Marko could, on a certain level, be considered the voice of reason. Vettel could not see Webber as soon as the cars drew alongside one another, because the high sides of the cockpit combined with the HANS device that prevents too much head movement both mean that Vettel was blind. He was, in some respects, running on faith when he passed Webber (just as any driver making a pass is). He certainly could have handled the pass better, but then so could Webber. In fact, given the information available to each driver at the time, Webber probably could have done more to avoid Vettel than Vettel could have done to avoid Webber. That said, Marko's manipulations came to the fore shortly thereafter.
I'm not denying that there were factions in play behind the scenes at Red Bull - but I don't think they subversively decided the championship. Christian Horner seems like a pretty reasonable guy, and his explanation of why Vettel received the wing in Silverstone made sense to me. Vettel was consistently faster than Webber in every sector in every session that weekend. He represented the best chance at victory, and Silverstone was the halfway point of the season. Red Bull lost their chance at the 2009 World Championship because Webber and Vettel were always too busy taking points out of one another than they were at building a campaign agianst Jenson Button. There was always going to be a point this season where Red Bull had to pick one driver regardless of how much they may have preferred staying out of it and letting the drivers decide on the track. I also think that Mark Webber handled the incident in Silverstone extremely poorly, playing the victim card straight away when he should have sat down and tried to work things out.