The mock trial was definitely not a good idea. First, it was organized by Brinker, the conventional straight arrow and "big man on campus." All along, Brinker had lacked the sensitivity to understand the nuances of the relationship between Finny and Gene.

It was especially insensitive to spring the trial on Gene as a surprise for which he had no time to prepare, suggesting that Brinker's motives were at least partially malicious. Rather than trying to bring about healing, Brinker seemed to want to nail Gene in a public way as responsible for Finny's shattering fall.

Neither Gene nor Finny were ready to confront what happened, and certainly not in the guise of mock trial with its structured need for a guilty or innocent verdict. If we value human life at all, the mock trial was a disaster on an even more fundamental level, as it led to Finny's fall, surgery, and death.

Brinker should have stayed out of it and let Finny and Gene work out their issues in their own way.

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.