We now have a new faction of SHIELD on our hands, led by Agent Gonzales. There are many consequences to this new development, all of which are positive for the show and the MCU going forward. With the threat of HYDRA neutralized, SHIELD under Director Coulson must move their chess pieces into position. This includes dropping secrets and opening a new door of transparency, as Agent Gonzales' points out. But it also must include an acceptance of powered people with special abilities, regardless of origin (alien or otherwise), as Director Coulson knows to be necessary. Rebuilding SHIELD will require the two factions (possibly more?) to confront each other. This will be ugly, brutal, but ultimately beneficial if SHIELD truly wants to destroy HYDRA once and for all.
We already know the players in each faction. Agents Fitz, Simmons, May and Skye are loyalists to Director Coulson's vision for a more integrity-based organization. A SHIELD that must operate in the shadows in order to save the world from threats it isn't prepared to handle. Director Coulson's team might have disagreements about how to handle powered people, but they agree that powered people should be handled on a case-by-case basis, instead of irrational generalizations. On the opposite side of this tattered coin, lies Agent Gonzales, a Nick Fury-detractor, who wants SHIELD rebuilt with a level of transparency that Fury knew was impossible to obtain. Agents Weaver, Morse, Mack, and a handful of anti-Fury activists make up Gonzales' faction. These agents hold an almost unshakable fear of power people. A fear that leads them to believe all powered people must be dangerous and eliminated.
These two differing ideologies must synthesize if SHIELD is to survive the coming bombshell revelation of the Inhuman society, but if they don't, and remain as that tattered coin, they will never be able to face the reemergence of the HYDRA threat. To do so, SHIELD must be willing to expose itself to the world, and prove itself as the protector it's always meant to be. They must also learn to embrace "special" people, or the world will never accept them. This will also play into the coming Inhumans story arc, as the Inhumans will not willingly accept SHIELD unless they prove to be a worthy ally in the fight against those who seek to destroy them. This is the coming battle. For SHIELD, unity must be the goal. Instead of secrets and spies, the two factions must unite as they hurtle toward uncharted territory.
The only question that remains, is if Agent Gonzales can put aside his disdain for Nick Fury long enough to realize the ally that he truly has in Director Coulson? The two men want SHIELD to thrive once again, and share a common enemy in HYDRA. Can these two leaders lead their factions, in unity against their enemies? Or will old grudges and old office politics cloud their judgement, which will further show the rest of the world SHIELD is not the protector the world needs or wants? Only time will tell, but as SHIELD battles itself, HYDRA is already regrowing it's heads of power and the Inhumans continue to pull individuals out of the fray, in fear of what human governments (and SHIELD) will do to their kind. The coming storm is brewing and it is up to everyone to insure that SHIELD can be a force for good, in a sea of very bad.