You asked for it...
First thing that comes to mind is replacing the towers holding up the JB platforms. Rather than that, what if the platform that the jailbreak tokens held up a cage wall that went all the way down to where the shield pack was, creating sort of cylander cells inside the base. Without the NoJailKill mutator on, inmates would still have a chance to be in the game somewhat, plus having them so close to the base would be a good way to display your trophies. Death by decompression (floor drops out) would probably be the easiest way to do executions, and in case of a jailbreak, a door would open and you'd walk right on to the bottom platform
Alternately, you could have both jails in the white area (shot00001), suspended over where the open holes are. Same basic ideas with the cages (or glass encasements, personally I like when inmates can try for frags) except since the cells would be suspended over the abyss, you'd have to double jump through a hole to safely make your way to lower platform.
Or, and from the screenshot, I can't tell where these three platforms are in relation to each other, but assuming they're in a straight line, you could create two birdcages to the center-sides. One to the left, and one to the right of the white platform, starting level to the megahealth.
Or how about doing the platforms in two layers, where the top layer would be the three screenshots (red/white/blue) platforms, and then underneath that would be the two jails, with the arena in the center-bottom?
How's that? Any help?