I somehow doubt we'll have a repeat of that. It fit into the overarching scheme/plot of DOS2 because of the Highlander-style "There Can Only Be One" Sourceror/god contest.
True, that was a natural fit within the plot for removing the companions you didn't select. However, there are some plot-related ways it could be similar here. For example, I doubt the tadpoles will be removed from everyone at the end of Act 1, because that seems like it might be the driver for the entire plot -- whether you use the power for evil, or fight it until there's some conclusion at the end of the game.
The companions you don't select at the end of Act 1 aren't likely to just drift off and leave the area with those things in their heads. Maybe the ones you don't pick will lose whatever temporary immunity is preventing them from turning, So they turn into Mind Flayers and you have to defeat them. That would be nasty, so I hope it doesn't happen. Not to mention a vastly overpowered group of enemies. But it would neatly solve the problem of where your non-selected companions end up.
ETA: It just occurred to me that this is even foreshadowed in the camp dialogues, with "what would you use to kill me if I turned?" and the rest.
