Since the group stage is coming to an end, I suggest we think about the second stage - the playoffs.
My proposal is to hold the second stage as a playoff among the top 8 in each group, with the first "evil" player playing against the 8th "good" player, and vice versa. Then, the best "evil" player from the group plays against the worst "good" player from the group (among those who made it to the next round). If there are not an equal number of "evil" and "good" players, then there will be matches between the best and worst players of the same faction. And so on, until the top three winners are determined.
The factions for the playoffs will be determined by the principle of each player choosing a "good" faction from 4 "good" factions, and an "evil" faction from 4 "evil" factions, choosing one at a time, starting with the red player.