I really like the "historic" quality of this mystery, it is instances like these that highlight the power of reason, to transcend historic forces and influences and re-create the past, I seriously hope future mysteries carry such interpretation-based elements.
Furthermore, a whole episode of dialog does not bother me one bit, because at this stage of reasoning, the fun is not in being hit over the head with dramatic twists, instead, interest lies in what new data is found and how it is interpreted.
As for what really happened, I think the "sacrifice" mentioned is not referring to Sekitani, but to someone else. I also believe, like some mentioned, that person died. If they were on the teachers side, the conflict would've escalated against the students favor, so I reckon it was on the students side which led to the school relenting.
The hyouka volume 2 cover depicts a wolf(?) eating a rabbit as other like rabbits are watching all around (sorry, forgot to screeshot), what remains is how Sekitani relates to the "sacrifice". Now, a common theme of historic distortion relates generation of myths and legends, in this case the great hero Sekitani, to the effects of mass desire and appeal. The non-violent hero is mentioned in outlets of student public opinion, but that is the "epic" subtly denied by the hyouka foreword writer, meaning only a few knew of the sacrifice, or the masses justified it for the cause.
Now, on the level of literary guessing, maybe Sekitani was not expelled but left on his own, only attending the Kan'ya to honour the sacrifice and "left us" being unable to get over it, or maybe the fifth day of hyouka involved a particular activity that was left out due to the sacrificed person not being there to hold/lead it. Well, past this point we can make up a lot of fan fiction.
By the way, are the texts (not the novel per se, but the documents they discussed) available or archived somewhere online? It is easier than re-watching episodes to go through them again to theorize before the curtain is pulled.