Right or wrong? Good or evil?
The usually distinct categories have gotten blurred in the post-Captain America: The Winter Soldier world. S.H.I.E.L.D. agents were the heroes of the universe, but now they're all viewed as criminals regardless of whether or not they support Hydra.
Coulson's as good as they get and even he's suspect. It's a crazy world. His friend, Maria Hill, brought Colonel Talbot to Providence to apprehend Coulson and his team in on Agents of S.H.I.E.L.D. Season 1 Episode 20. Coulson couldn't allow that to happen with Skye out there.