Ugh.
I shouldn't have watched Ultron tonight. I won't spoil anything in case you haven't see it but Coulson's (in the eyes of Gonzalez and his Real!SHIELD allies) make so much more sense in the finale and ending scenes of the movie.
Obviously the movie doesn't mention Coulson specifically, it connects a lot of dots in the show.
Spoilers [Spoilers] 1. Around the middle of the movie, Fury appears for the first time to the Avengers and gives them a pep talk and discusses with them on how to bring down Ultron. He them announces he's leaving with Maria Hill, and Stark makes a cynical and suspicious remark, believing she was always in Fury's employ the entire time. (Much like how, Coulson is in Fury's inner circle). We don't see him until the final arc of the movie ends with a giant SHIELD Helicarrier helping evacuate Sokovian citizens from their nation/city, which has been lifted far above the clouds by Ultron(who is intending to smash the immense landmass into the Earth, creating an extinction-level event that will wipe off all life). While the episodes themselves aren't out yet, I am heavily biased towards the idea that before and concurrently with the movie, Coulson settled out any internal fighting and was contacted by Fury to pilot one of his (seemingly limitless) Helicarriers, and that he, his SHIELD team, and any defectors from the Real!SHIELD were the ones piloting and defending the Helicarrier from Ultron on their way to Sokovia.
Basically, all of this leads me to believe Coulson's going to come out on top at the end of this season, and the hypocrites, myopic rogue SHIELD agents, and bigots like Gonzalez, his allies, and likeminded SHIELD agents will be killed or left in the dust. (/spoiler)