Regardless of whether Whedon will direct it, i disagree that the studio would not make the film based on Robert Downey, Jr. + his potential salary requirements
a) Obviously, the Avengers movie had been given some thought before, as they included the Nick Fury cameo in the first picture - and have laid out a timeline for the Hulk, Thor and Captain America pictures - i've seen it on imdb since - well since iron Man was released. Furthermore, with potential franchise pictures like Iron Man, the contract will usually include holding the actor for sequels, in this case, the Avengers movie may have been included.
b) Downey was making yet-another-comeback when he got hired for Iron Man. It may not have cost the studio too much (relatively speaking) to tie him down to a multi-picture deal.
c) I disagree that the franchise is risky. Even if the Hulk underperformed, Iron Man has HUGE buzz. I think it would take Thor and Captain America to tank for the movie to be pulled, otherwise, the script will be written to emphasize the money makers and scale-back the bombs.
d) as for hanging in limbo. the thing to remember here is that Marvel was a major producer for the Iron Man film, and they moved into film production over licensing as a way to gain greater control over the brand. Marvel has an entire Universe of characters, but when Spiderman is a property at Sony and Daredevil (quality-aside) isn't, then it becomes nigh impossible to even acknowledge the other superhero, even though they both live in the Marvel Universe "New York". Marvel is going to want to homogenize their universe, there are too many potential franchise tie-ins to let loose. The aren't a traditional studio in that they are looking for the next English Patient or Benjamin Button. They have 60 yrs of IP to bring to film, and it behooves them to work it, both because superheroes still bring in the money and because it helps (re)expose people to comic books, still their main line of work.
My pet theory is that the Avengers movie was the starting board and then someone said, "Hey wait, let's do an origin pic about each of the heros and we'll make 5 times the money" Plus that streamlines the Avengers. The audience will be familiar with the heroes, and they can get straight into the story.