First off, here's the player detector:
Nothing more than a simple redstone torch 3-clock located well outside the range of the admin anchor whose aura you can see at left. For the purposes of placing this, be aware that the radius of the anchor seems to be 5x5- make sure there's two whole chunks between the anchor and this timer.
The command block you see there is configured to /say Timer tick whenever the timer ticks.
Now, here's the chunkloaded part of the circuit:
The signal from the timer comes in at the top of this screenshot. The first thing it encounters is a pulse generator with a 3-tick repeater and a redstone torch, which ensures that the next part of of the circuit can never receive a constant ON signal, no matter what phase the clock gets stuck on. It could be replaced with a single pulse former gate from your favorite RedPower clone.
Whenever this pulse former emits a redstone pulse, it triggers the command block nearest the top of the screen, which prints "Pulser tick" in the chatbox.
Next up is a sort of pulse lengthener circuit, consisting of two vanilla repeaters. The first is set to a 3-tick delay, while the second is set to a 4-tick delay. The 3-tick repeater lengthens each pulse coming from the pulse former a little bit, then the 4-tick lengthens it a bit more, with the effect that the successive pulses all get blurred into one. The second repeater never actually turns off as long as the timer keeps ticking. Don't ask me why this works; it just does.
Following that is a delay circuit not so different from the one shown earlier on the home base side. Whenever the second pulse-lengthening repeater is consistently ON, the right hopper is disabled and the left hopper is enabled, so the 60 cobblestones all flow into the right hopper. When the pulse lengthener's output turns OFF, meaning that the timer offscreen has stopped ticking, the cobble will start to flow into the left hopper. When the right hopper is completely drained once again, the comparator will cease pushing a signal into that grass block, allowing the redstone torch to turn on and disable the admin anchor.
I didn't end up having to edit RC's config files or mess with infinite item sources at all. The admin anchors can be turned off with a simple redstone signal just fine.
The command block next to the redstone torch prints "Disabling chunkloader" in the chatbox, so I know when that happens.
All of the circuitry in this screenshot could be boiled down into a single Pulse Former, a State Cell, and a NOT gate. Take the signal from the timer (which could itself be replaced with a Timer gate), run it through the Pulse Former, then immediately into a State Cell with a delay of 30 seconds. The "front" output of that gate (the one that turns on the whole time the state call is running) can then be inverted and fed into the chunkloader. Whenever the timer ticks more than once every thirty seconds, the State Cell produces a continuous positive output; this turns the inverter off and allows the chunkloader to run. When the timer gets stuck, the pulse former stops pulsing, so the state cell eventually runs out and turns its output off; the inverter then turns on and disables the chunkloader.