And Stark did kill Vanko and got away with it along with several AIM operatives in Iron Man 3.
You mean when he saved the President of the United States?
Iron Man may not directly report to the president or the government or whoever, but he operates with at least a partial blessing from the government. Black Widow still went before Congress after the fall of Shield, and Maria Hill went before congress after starting her new job working for Stark. There may not be an official chain of command, but there is a working relationship.
Meanwhile, Talbot and members of his team all seem to know about Coulson and are now willing to work with him, including passing along both information and assets. Coulson's existence certainly isn't a secret that zero people on earth know about.
On the face of it, it's been assumed that Gonzalez has the backing of the US govt, though without any onscreen proof yet to back up that assumption.
There are a number of possible outcomes here, with varying degrees of destruction and or cooperation involved, but I think my top two perferred outcomes to the current story would be:
-Gonzalez runs the official giant Shield organization, with a friendly working relationship with Coulson who is in charge of a smaller more covert team
or
-when the Avengers take down Baron Strucker in about 5 weeks (or at least we assume they will) we hear EJO say the infamous Hail Hydra line and all hell breaks loose in a battle between the now clearly defined good guys and bad guys
Of course there are many other possible outcomes too. Here's a thought that just crossed my mind: what if GonzalezShield isn't bankrolled by just the US govt, but is also funded and backed by Tony Stark? That could be an interesting conflict down the road.