Fuller said he intended one thing but the relationship wanted to evolve in the other direction and he let it. There is some fanservice to his comments via Twitter, but saying their relationship could easily become sexual was in a real professional interview. Letting a same sex romance evolve naturally isn't just appealing to people who want 'wanking' material.
He can say whatever he likes after he wrote and filmed it, it doesn't change his original intent.
Will's true connection was always with Hannibal. He wanted to fall for someone like Alana because she represented the parts of himself he was running from. S3 shows us that Will chooses Hannibal over Alana when it matters, so when we look back on S1 and S2, who is it he really has feelings for and who is he really jealous of in the Hannibal/Alana situation? I think the moment when Alana comes to find Will moping in Hannibal's kitchen and he totally dismisses her gives us the answer. He doesn't pine over Alana like that. Even Alana realized near the end of S2 that something far more was going on with Hannibal and Will than she realized and that it wasn't about her. You can see it when they have dinner together. The Alana crush was like his marriage. Will was running away and trying to hide from who he is. S3 even made a deliberate parallel to Will being a closet case.
Will was deeply traumatized and mourning in the beginning of Season 3, it makes sense that he's pushing people away. I'd say he's less hung up with missing out on a serial killer romance and more upset that he not only let Abigail suffer in the clasps of a psychopath for however long Hannibal had her, but that he also failed to save her, again. The second half of Season 3 is Will being dragged back in because Molly convinces him and then, after a brutal attack on his family (that Hannibal is responsible for) realizes that they're no longer safe until A. he leaves them or B. Hannibal is dead. You can interpret the series as Will being mind raped into entering a romantic relationship with a psychopath but you can also interpret it as Will seducing and deceiving Hannibal and successfully killing him.