kirk55555, where are you getting the idea that Gonzales wants to destroy Coulson, or that Mac and Bobbi want to take him down "with extreme prejudice"? Putting someone other than Coulson in charge of SHIELD doesn't mean putting two bullets in the back of his head.
Because Mac and Mockingbird keep talking about how they're going to take SHIELD down? The only way to stop Coulson/May/etc from staying in business is to permanently take them down. If Gonzales's group was willing to do something less extreme, they'd actually talk to Coulson, not infiltrate SHIELD for the stated purpose of taking it down.
I'm pretty sure Mac has been wanting to do that for awhile. Maybe he's going to at least try to kill Skye (probably with Simmons help, since Simmons is about ready to become the MCU's equivalent Bolivar Trask anyway, except she probably hates inhumans more than Trask hated mutants) and that might be when Skye starts getting control of her powers, leading to a victory for Coulson and his team and Gonzales and his friends getting locked in a deep, dark hole. I don't know, it could go several irritating ways.
Personally, I'm hoping for Mockingbird, Mac, Gonzales and Simmons dead, Skye in control of her powers and Coulson's SHIELD coming out on top. I doubt it will happen though, and I think that the most likely scenario is the season ending with Coulson's SHIELD destroyed, Skye a prisoner of Gonzales or reluctantly teaming up with her Dad to escape him, all leading to Coulson's team reforming (again) and taking down Gonzales's team next season.
Regardless, while I really enjoy AoS I think this idiotic SHIELD vs Fake SHIELD story is the worst thing since the first part of Season 1, and I don't think the show will ever be able to work with Mac and Mockingbird after the story arc (assuming that they, unfortunately, survive the storyline).