I’m not convinced that eating prion-contaminated tissue is a major factor in transmitting prion diseases. Prions are still proteins, which are broken down to amino acids very readily by the digestive system. Even if prions are more stable than most proteins because they have formed these crystalline-like oligomers, such large molecules would have little chance of being absorbed intact into the bloodstream. Instead, I would imagine they would pass through the digestive system and be excreted in feces.
The Wikipedia article on kuru proposes an alternate mechanism which seems more plausible to me:
the strong possibility exists that it was passed on to women and children more easily because they took on the task of cleaning relatives after death and might have had open sores and cuts on their hands.
This would allow the prion particles to enter the bloodstream directly where they could be absorbed into tissues and persist for a long time, bypassing the digestive system entirely.
If this is the primary mechanism of transmission, it would support your argument that eating cooked meat would have minimal risk, while handling diseased tissue would actually be the much higher risk activity.
Do you know if any of the 200 people who came down with BSE were involved in handling/butchering the meat, as opposed to just buying contaminated meat at the store and eating it? (I suppose people who bought meat at the grocery store could have still gotten infected during meal prep, but if a substantial number of victims were butchers/slaughterhouse workers/etc., it could be evidence in support of this hypothesis.)
I was thinking more that the acidic environment of the stomach could break down the aggregates to the protein monomers. This step wouldn’t be reliant on proteases, although proteases might then be able to further break down the monomers. But I haven’t looked into whether this has been studied.