Step 1: Knock her out. Sleeper Hold, Pistol Whip her in the temple, what ever, just get her no longer awake and do it quietly as possible.

Step 2: Leave, with her. When she wakes up make sure she'd bound, gagged, has a weapon trained on her face, and a translator handy to explain "Don't move, we've got a little something to show you that's just a bit important if you want to keep your amazon's form getting wiped off the map."

Step 3: Show her. Show her what Nukes can do. Show her what Higher caliber Supers (those flying bricks you mentioned in the OP and the like.) can do. Show her how many Chimera's are out there. And then through a translator explain to her she can stop doing the horrible things she's doing and abdicate to someone else, whom you will designate, or all of this insurmountable power will be brought to bear on her Amazon's with no quarter asked or given. There won't even be memory left of them by the time it's done, they'll even fill in the hole in the ground, put down training expenses in the finance books, and no one will know about it in a few generations. It will be as if they never existed if she fails to follow your instructions, precisely.

Then go back with some people observing form a distance and one or two of those flying brick types as insurance to make sure she does it.