Well, it (the 57m drainage channel) actually did go under the temenos wall, on this point the channel was cut in a single block 2,50 m long and 1,25 m wide. see: Michael Neumann, "Kanalisationanlagen, Wasserleitungen un sanitäre Einrichtungen im pharaonishen Ägypten", Wien, 2008, page 20.
Water was never supposed to enter any mortuary temple via the pyramid courtyard. There is no evidence that drains were blocked as you describe it.
The drainage channels in the pyramid courtyard of the Sahure and Niuserre complex were not very deep but increase in size the closer you get to the temenos walls, they do lead the water outside underneath the temenos wall. See work mentioned above page 22.
Mortuary courtyards were somewhat lower than the surrounding colonnades in order to prevent water from flowing into the rest of the temple. Example of Khafre: pyramid courtyard was 5cm deeper than colonnade; in the courtyard was a drainage channel that went under the walls to the outside. See work mentioned above page 29-30.
Fifth dynasty mortuary temples had a water collection basin of sandstone (100 litres) in their courtyards, the floor of the courtyard was slightly inclined to the middle. A drain led the water to the outside. Most complete examples found in Niuserre and Pepi II complex.
See work mentioned above page 31.
I doubt the roof of Khafre’s mortuary temple had holes in it, the roof would have been constructed to evacuate the water as quickly as possible. It probably had similar drainage systems as the roof of the valley temple, here the roof consisted of several levels, with the aid of ramps and steps the water was led to lower portions were it was collected by drainage channels that led to water spouts. See work mentioned above page 11.