Just a quick reply here, will try to get a more detailed answer later.
From memory, the brake disconnect tool goes into the NORMAL brake line at the normal brake control module. In effect NORMAL brake pressure is prevented from operating the deactivated brake.
However ALTERNATE brake pressure can still operate the relevant brake. Under usual circumstances this this means the brakes are operated (by the alt system) on gear retraction.
So, the rule of thumb is........
Brake leaking or hoses leaking, cap the line (upstream of the leak of course)
Speed transducer u/s or a/skid problem, De-activate via disconnect tool.
You may find the extra penalty for a capped brake is in fact due to t/o performance not brake efficiency as if the brake is capped then the gear must remain down for 2 mins prior to retraction to ensure wheel rundown.
This may be wrong of course as I don't have a DDG or MEL to hand to check my data.