In my sight, I think we've triggered what is essentially meant to be an endgame event very early. Every previous Spider-Man game has been a game that's meant to go long, and has gone long, and every time there's been a minigame about finding out something other than alignment. In Maximum Carnage, it was how to dispose of the seemingly invincible Carnage. In Hobgoblin, it was the identity of the mysterious Hobgoblin (Related to catching scum, but not perfectly). Here, it was discovering the True Spider-Man, which was a prerequisite for the Trial event firing. Because of what happened with me N1 (which was opening Pandora's box, seeing how many false spider-men could have turned evil) the identity of the True Spider-Man became known far before it probably 'should' have been. Because this information became, on d2, not just spider-knowledge but public knowledge, Minish and Traveler were able to reach out and get the party started essentially as early as was mechaically possible. Because of that the "threat" of an innocent claim from Spider-Man is not as great as it was probably intended to be (since there are few scum and fewer town dead, rather than an endgame scenario that might have created an instant scum win on Innocent), and the reward of Guilty, to the town, is much higher.
Looking at it from a design perspective, it seems like it was meant to makes Spider-Man largely choose between giving the Scum team a huge, possibly insurmountable bump but retaining his own ability to win with the town and, on the other side, giving the town an easy path to victory at the cost of (possibly -- I do think we don't know if Threat spidey himself gets a different WinCon) losing his own. Late enough in the game it becomes lose-lose for Spider-Man, the sadistic choice it was meant to be: lose with the town when all the villains come back, or probably lose as scum when he's the last that remains.
Walking this back a bit, let's think about the scenario that I, at least, would predict as a game designer: the one where instead of Spider-Man being willing to sacrifice himself for the good of the Town because he's a hero and that's what heroes do, the one where he plays to his win-con at all times. In that case, both pleas make sense. Early game, a self-interested Spider-Man would want to plead Innocent, dealing the game a small hit, but one that's recoverable because, hey, we already know who dead scum are, the whack-a-mole motions shouldn't take that long. Late game, he'd want to plead Guilty: If there are enough dead that bringing all the scum back would deal town an immediate loss, then it would be easier to win as self-scum, because winning as town would be 0%. In either case, it has a shake-up outcome on the game, but the integrity is preserved.
We stand to benefit greatly because Silver has expressed a deep willingness to do what might be the irrational thing, taking the guilty plea while a) the details of the trial are in the public eye and b) the alternative is not a game-losing proposition. I believe strongly that this should be let happen.