Tony alone has access to all of SHIELD's secrets. Tony alone has been known to run a large organization with loose ties to the military. Tony is the only one whose walked onto the helicarrier and stared giving orders and trying to figure out how Fury runs things. Him being anti-establishment doesn't prevent him from giving
orders in establishments, or else he wouldn't have a huge company. It'd be a good story... too bad there's not a comic book story to draw from on that issue.
I think a War Machine cameo could be pretty awesome. It's never too crowded for a plot-relevant cameo.