1) Solving the Godsmen murder: I turn in both Thildon and Saros, but not Bedai Linn. Then I become a Godsman. Then, if I talk to a worker on the secret project and ask about the engineers, the worker says, "Well, you already know Bedai Linn has been arrested. Who would have guessed she's a murderer?"
Good catch. Fixed.
Also, when I talk to Bedai Linn again, she acts as if the murder is not solved, and my dialogue choices are the same as when I was interogating her for the murder.
I'm having trouble duplicating this. Once you're fully a Godsman, Bedai should ask you "So, you're a Godsman now, are you happy with it?" and, if you answer correctly, give you the Sabotage quest. It is still possible to have some responses regarding the original murder quest, mostly of the "Thildon says you're an Anarchist" variety. I think it's intentional that those be available until there's no longer any question about it, though I agree it's a little odd after you've completed that quest.
2) After talking Sandoz out of suicide, shouldn't there be new dialogue with his daughter, who helped me? I seem to remember it being there before, but I can't swear to it. In any case, right now she and TNO have no new dialogue for each other after saving her father.
The dialogue initially remains the same, but once you're fully a Godsman, some of her replies will change. Perhaps if at this point you weren't really fully a Godsman yet (as the Bedai problem seemed to imply), it would explain why you didn't see it.
Qwinn