In A Separate Peace, the mock-trial is certainly cruel. It is cruel to Gene and probably even cruel to Finny. There are better ways to handle such things.
At the same time, one can argue that what Gene did needed to be exposed. Although there are better ways to expose him, one could argue, at least the trial results in his being exposed.
An actual civil or criminal trial would have worked much better. Finny would have been surrounded by people who would have prevented him from panicking and falling down stairs at an actual trial, for instance, and he would have been somewhat mentally prepared for the result.
Ironically, what Gene does to cause Finny's accident is so unexpected and so hideous that none of the adults that are in a position to question the accident even consider the possibility, as far as we know. If they had, Gene and Finny wouldn't have been left at the mercy of Brinker's arrogance, and the result wouldn't have been as tragic.