I don't know who said it but that article in the OP is as much commentary/speculation as it is "facts". Could very well be plenty or very little true. What makes it a fun read to buy into is that those of us following this path towards Avengers have seen how Marvel has handled things. i won't rehash what's been said. Marvel may or may not need to pull back the reins on how they are handling things.
The Favreau stuff was out there as well as the dealing it took to get Sam Jackson on board. Even before it was official many just sniffed something was off when Norton wasn't signed on after weeks of expressing interest. Yet still they got stellar casts for both Thor & Cap and got Renner to sign for Avengers.
Lets see who they get for Runaways, granted it'll be largely unknowns but we'll see.
Also, I'm not of the camp that IM:2 is a bad film even a disappointment creatively(I was rooting for $350m USdom but I digress). As far as any truth in Marvel meddling storywise to get the Avengers links in I don't see it as jarring at all. Could a few elements have been tweaked, sure I suppose.
A tweak I'd have made would be to have that black market passport runner prominently wearing a big ring and verbally saying, "An enemy of Starks is a friend to the Ten Rings, good luck." Or something to that affect, instead of reading the intent of that scene in an interview.