How come the aliens let him go?

Uh,no we don't. We tag some animals with GPS trackers and release them so we can follow their migratory patterns. Some of those are even killed later to check for toxins or stomach contents. Unless aliens are abducting people to insert completely imperceptible tracking devices, it makes no sense that a species capable of interstellar travel spends its time hovering around Earth, mutilating cattle, rectally probing humans and flattening crops.

They're coming to get you, Barbara!

Most people who are abducted are implanted and repeatedly abducted as are their children's and future generations so whatever it is the aliens seem to be conducting some multi generational study of the human race and perhaps slowly genetically altering us.

The Travis Walton case is rare in that it was a one-time abduction as far as we know. Travis speculated that perhaps he just unintentionally came across the UFO and when he got close to it it accidentally harmed him and then the aliens had to try and patch him up before returning him. Although the movie actually differs a lot from his actual account and is a highly sensationalized version.

Travis himself explains it in many videos available on You Tube: they didn't mean to take him as part of a plan. Travis thinks that he himself blundered into some unknown ufo-function when he was either accidentally hit by the beam; and that the occupants, when they noticed that he had been injured, took him aboard to save his life. He refers to it as a kind of emergency-ambulance-type of rescue, sort of forced on the aliens because of his blundering tom-foolery. In like manner, they released him when they determined that he probably was not going to die, and had regained enough stamina to be released from the ship.