The entire thing was horrible and profoundly unethical. His brother has stated it really changed Kaczynski.
Some people have claimed that it was run by the CIA as part of MKUltra. This is certainly possible but not really substantiated by clear evidence as far as I've seen, and even if the CIA has some relationship they probably didn't instigate the experiments but just asked for research notes or something relatively benign like that. We'll probably never know for sure though.
Whatever the case may be, of the group of students that were subjected to these abusive experiments only one became a terrorist, so "the CIA created the Unabomber" is rather simplistic IMO. The primary blame remains with Kaczynski, no matter what.