Idunno... seems like way too much trouble to go to if you're only concerned about <100kHz. The above circuit and discussion seems applicable to VHF noise problems (with the difference that, an op-amp won't do anything up there).
Would the 3.6V "low noise" supply happen to be the same as the charge pump supply? Don't neglect induced supply ripple; the charge pump needs to be very smooth and/or very well filtered to keep from affecting that.
Cap multipliers are excellent, as far as I know. This guy uses them religiously:
http://electrooptical.net/ he's fond of using 2 or even 3 transistors cascaded, with a common RCRCRC filter chain. (Note that you only incur one Vbe in this configuration, plus a modest Vce for each transistor.) The base filtering, plus double or triple duty against Ccb and Early effect, kills noise hard (80dB+).
But again, that's in the MHz, where these sorts of steps are necessary.
Regarding the gain, you've got a CCS (common base) feeding a CCS, so the voltage gain of that node is tremendous (set by (load resistance) * (pass transistor hFE), which will be pretty high). Agree, common base is a good level shifter. In light of the gain problem, though, better would be an inverting configuration with shunt feedback, so it has a CV output instead of CC, and the voltage gain is fixed. Then swap the op-amp inputs to get the right feedback polarity, and all is well.
A low output impedance also has more immunity against ripple in the CCS. And note the CCS will have ripple for the same reason that the pass transistor allows noise through: Ccb and finite VA. Also a small input from base supply voltage, which will be relatively small because of the zener. Hmm, if that's a low voltage zener (under 5V), it won't be too much less ripple than the same circuit using two diodes in series as bias, really. A red LED might be good to use, they're about as stable as a zener diode (or more stable, maybe?), but have lower voltage drop (~2V).
If truly your only problem is under 100kHz, would it not be easier to run the switcher(s) fairly fast (some MHz), and use a tight control loop there?
Tim