If the last surviving human mutates to an alien, do they win with the aliens?
As written in the rules book, humans loses only when killed by aliens. Therefore it seems logical that a mutated human wins with aliens even if he is the last one.

Said this, I agree with you, this is definitely an unsatisfactory winning. To avoid it, I suggest you to set as "house rule" that the Mutate card cannot be played by the last human. This will make the human to fight for his life!