I have GTW installed and rarely have any issues with unwanted aliens in my game. I have even played a scientist to level 10, had him travel to Sixam, marry an alien and produce offspring with her. That was the only story-line I wanted the aliens in and I am still playing the same save file 3 generations later, I don't have any overproduction of aliens.
If you want to avoid aliens then don't go to any bars on alien night, if you do by accident and a bunch of alien townies are spawned delete them using manage worlds, and if your sims is being abducted use the sim reset cheat to cancel out of it with no pregnancy.