But are you sure the number is not just unacceptably high because [...] many of them would have to have been seen as having substantially greater than 13% chances of innocence? If not for some biasing effect like that, it's hard for me to see why the moral question would suddenly be clear once it was stated in population frequencies rather than in individual probabilities.

Well, people's intuitions about justice aren't all that consistent, so I don't think this particular moral question is going to suddenly become clear to all observers no matter how it's stated. That being said, though, I don't think we have any particular reason to think that Guede was convicted on unusually shaky evidence, so it seems reasonable -- given certain assumptions -- to take our estimates of his case as representative of murder cases in general.

A 13% innocence threshold for each particular case won't give you a 13% innocent prison population (assuming good estimates, which is probably generous in this context), but if we adopt that criterion and Guede's in the middle of the probability distribution for murder defendants, it seems likely that the resulting population-level incidence would still land on the bad side of 8 or 10%. Which doesn't look much better.