There's an enormous difference between something that's controversial enough to get local activist groups to oppose it, and something that's controversial enough to prompt some unnamed government agency to kidnap somebody's daughter to stop him.
Being connected to the nuclear problem doesn't prove kidnapping--it just proves a connection.
Perhaps Lynne really did just run away; if there's any chance she was caught up in the anti-nuclear activism on campus, she'd certainly have had many reasons to feel conflicted, ashamed, scared, confused...
What would it be like to know your dad is responsible for the two things everyone on campus hates most--unethical nuclear weapons and unsafe nuclear reactors?
What did Lynne know of Otto's work, I wonder? If he was preparing testimony for the ECCS hearings, she may have been aware of the sole issue: reactors weren't safe, and the ECCS hearings were likely to prove that.
The people trying to protect the mountain were talking about things like disturbing the earth and mild contamination of the river; what kind of energy would their movement achieve if it were revealed that this was not about "marring a state historical landmark" but rather the fact that a cooling system failure could result in a Fukushima-style radiation catastrophe?
Lynne's father was not only privy to those safety assessments--he had been conducting them since at least 1959:
http://www.osti.gov/scitech/servlets/purl/4260314/
From her parents to her siblings, all are/were accomplished, educated professionals; there's no reason to think Lynne was wired any differently. As the second oldest, how aware was she of her father's work? To what degree did she understand it? What shock might it have been to her to move from Simsbury--basically a bedroom town for Combustion Engineering and other nuclear operations--to a liberal campus where she was suddenly the daughter of the enemy?
Except, her dad may not have been the enemy. A major, major threat to the industry's case was the fact that individual nuclear scientists were planning to go on record during the hearings, averring that nuclear power was NOT yet safe, that the cooling systems were a colossal failure.
Protecting a national landmark from truck tire tracks is great, but what if you have inside information from a student, or students, that federal hearings are about to take place during which whistleblowers will destroy the myth that nuclear power is safe?
The timing of this is just way, way to close to overlook. Sure, Lynne could have run away because she didn't like math. She could also have run away, or come to some harm, because she posed a threat to the nuclear industry, or because her father needed to be persuaded to stay on the straight-and-narrow.
I am truly open to all theories; but in a world where we don't even have proof, beyond hearsay, that Durst ever set foot in Vermont, Lynne's father's status as a powerful player in a critical, besieged (need I say multi-billion dollar) industry surely can't be overlooked.