It's assumed that Nathan dies if you destroy Raven Rock or gets executed later on. Anna Holt works for the Enclave -- good for her.
And how good was your karma? You may be Last, Best Hope for Humanity but you may have been only slightly good, so being a meanie to Fawkes may have knocked it down. If your Karma level was at Very Good, then I can't see what you might have done.
here's something interesting, i have played through the main quest quite a few times and i have seen nathan at raven rocks lots of times, i have seen him get killed there and i have also seen him get wounded and not killed before i killed the enclave who shot him, that time when i got back to megaton he only had like 2 bars of health left, so he made it back that time, i have seen him back in megaton most of the time i get done with the raven rock quest, but a few of the the times i never seen him again, so i'm not sure if its a glitch that he makes it back alive, and when he does make it back alive, if you talk to him, he still likes the enclave just like he did before, how or why he ends up at raven rock, i have no idea. but usually when i'm at raven rock i quickly get to level 2 of raven rock so that nathan doesn't get killed by the enclave because if you hang the area he's at, his cell doors opens and the enclave kill him.