Brakes? We don't need no stinkin' brakes!
You bring up a good point. I wouldn't rely 100% on ESC braking when it comes to something with that much kinetic energy, not with modern ESCs at least. I'd set the brakes to 10-20% on the ESC and come up with some mechanical brakes that will work. Running brake discs at the center diff like it's supposed to be will interfere with your gearing options unless you go for some really puny brake discs. I think I'd go with brake discs on the diff input cups or even 4 wheel braking. It'll take some work to figure it all out, but this conversion is going to be worth it.