What incentive do humans converted into aliens have to keep playing?
Consider a special rule used in some scenarios for Betrayal At House On The Hill.

If a player is "converted" to the Traitor side, they will lose despite a Traitor win, unless they can demonstrate that they have notably contributed the success of their new side - this invariably means either killing or converting another player who has not yet joined the Traitors.

This provides motive for any players converted prior to the endgame. They can still win if they begin playing in favour of their new side as quickly as possible, and achieve results for them.

Applying a similar condition to humans-turned-aliens would allow almost all players a second chance to achieve a victory in some way, and reduce the number of players unable to win, and reduce the time of play in which it is known they're unable to win. You could consider including any other important milestones as counting towards this condition.