I dont think Will's idea of family as a "foreign concept" has really changed that much, which is why he is awkward in all his family interactions that were shown to us. He is using a lot of strength to just let himself be a part of it, but it does not come "naturally" to him - he does not say 'i love you' back to molly, he isnt very physical with either her or Walter: even when he imagines them on the bed together while theyre talking about dog's balls, there's closeness between them, but no real intimacy. The only touching we have seen between them was the neck-cheek brushing at the very start of the GRD arch.
Will does feel "natural" with Hannibal, because the "alone together" thing they have going on is something that does not require his active strength to participate, and he is always accepted as he is. The difference being that Hannibal would prefer (or simply would not care if) the rest of the world outside their bubble to burn, while Will (still) wants to actively protect it - both from Hannibal and from himself. Hugh plays this anguish so well - with both Walter and Molly. He always feels responsible, especially when it involves Hannibal's activity towards that outside world. And Hannibal knows this. He didnt care if D killed Molly and Walter, he knows that the intrusion is enough, and that Will's mind and empathy will do the rest, and Will will start severing his ties to his family. Hannibal knows, or can predict with great enough certainty, that Molly can not be as stable and offer a total of an acceptance of WIll as Hannibal is. In the hospital, Will understands that Molly's promise of still being the same when he does come back is impossible. It will never be possible. When Hannibal asks him what did he see in Molly now, Will knows that Hannibal already knows, he sees the world touched by violence, shaken and ruined and changed by violence that Will (feels) brought with him.
So, of course, Hannibal quotes Faust to WIll ("Two souls, alas, are dwelling in my breast, / And one is striving to forsake its brother"). Faust is the ultimate symbol of not being able to accept your own limitations, and going metaphorically beyond humanity with trying to find ways to overcome them, to the point of contemplating suicide when all tries had failed. Until a literal "beyond humanity" option is presented to him, in the form of Mephistopheles. Those two souls are the ultimate options for Will, and Dolarhyde too (if anything, we can count on Hannibal to always cover many trains/tracks of thought): Dolarhyde is ascending into the Great Red Dragon, and Will must accept that he cannot protect the world, either from Hannibal, or from himself. Will's quiet stream can never be real, it will always be a fantasy of death. His nightmares, on the other hand, will always be more real that anything else in his life.