I don’t know about this, though… it actually seems to me that the “Bedelia’s patient’s death” backstory was the only part of Bedelia’s arc that was planned in advance, since it was teased from the first in S1. I think the plan was always to make audiences suspect that Hannibal had killed Bedelia’s patient, only for it to turn out that he manipulated her into killing the patient. That’s in line with Hannibal’s modus operandi, that was also established very early on.
The parts of Bedelia’s arc that were not planned (as confirmed in various interviews – I read’em, don’t have links unfortunately) were, firstly, that she ran away in S2 and had to be brought back by Jack; which was determined by Gillian’s availability that season. If Gillian had been available for more episodes, I think the plan would have been to keep Bedelia in place in Baltimore as Hannibal’s therapist through all of S2′s shenanigans, and do the full flashback reveal when Jack brought her in for questioning toward the end of the season. At that point, it was stated that Bedelia had killed her patient, and also that he had choked on his tongue “not attached at the time,” so showing the event in S3 is really just horror show set-piecing, with some minor shading as to Bedelia’s psychology.
The second big part of Bedelia’s arc that wasn’t planned was the Florence trip, because to a very late stage in story development, it was supposed to be Abigail. They made the choice to kill Abigail to tie off the “full circle” Mizumono narrative, but still wanted to keep the plot point that Hannibal would escape with someone who wasn’t Will (very hard to write S3 if he couldn’t at least have a conversation with someone who knew about the events of S1-S2!), so that person ended up being Bedelia.
I hate to say this, because it was such a great emotional beat and a large part of why fandom really loved Bedelia’s character in S2, but the part of Bedelia’s arc that doesn’t “fit” with the rest is when she went to visit Will in jail and told him she believed him. That scene exists so Bedelia could have a “mic drop” moment as she temporarily left the narrative. Meanwhile, a scene was cut where Bedelia discusses Will with Jack and proposes that Will could be a psychopath masquerading as a sensitive introvert.
If you imagine Gillian as a consistently available guest star in S2, you get a much smoother character arc. Bedelia already clearly knew Hannibal was “dangerous” by the S1 finale, that he had a pattern with “violent patients,” and even seemed to suspect something was up with the food. The only reason she might have panicked in early S2 was realizing that Hannibal was the Ripper when she didn’t before, but that’s a reasonable headcanon – it’s not in the text at all. It actually makes more sense that Bedelia would have forged on as Hannibal’s therapist, an increasingly rattled and frustrated voice of reason trying to protect both him and herself from his life-unravelling obsession with Will. The only person on Hannibal’s side, for all the good it does him since he refuses to hear her advice.
That’s not to say that Bedelia wouldn’t have recognized similarities between herself and Will as survivors of trauma caused by Hannibal, in this scenario, or that she wouldn’t have wanted to see him for herself, or even that she wouldn’t have told him that she believed him. But the jail visit scene implied a potential trust and alliance between Bedelia and Will that I think ultimately was never there. Bedelia never saw Will as an oblivious innocent – as far as she was concerned, Will had to be a master manipulator on Hannibal’s own level in order to get Hannibal into such a tizzy. (I’d call this bias on Bedelia’s part: I think she genuinely couldn’t believe that Hannibal, a customer as cool as herself, would up and lose 100% of his chill without someone at least intentionally trying to make it happen.) She tells Hannibal as much in S2E1, and that they “deserve each other,” and if she’d stuck around to see the rest of S2 first hand, she would only have been further confirmed in that low opinion. It’s even worse that Will turns out to be both a master manipulator and a quivering puddle of raw emotion, because he can’t be trusted to stick to the law, or enlightened self-interest, or vigilante justice, or anything – the reckless unpredictability Hannibal loves is precisely the thing about Will Bedelia can’t stand, because he’s apt to ruin Hannibal’s life at any given moment without notice, and if Hannibal’s life is ruined, Bedelia’s life is probably ruined, and that’s been true since S1. It wasn’t Hannibal driving Bedelia to drink, because she’d been dealing fine with Hannibal for years and continued to deal with Hannibal just fine. It was always Will.
A further train of thought would be, if Abigail had lived and gone to Florence, what would have become of Bedelia. I suspect that’s a question that no one can answer, because they were going to leave it up to S3 anyway – Bedelia might have just peaced out into FBI protective custody, as Alana and Margot peaced out of the narrative in the S3 finale. The worst case scenario would be that Bedelia was supposed to die in the S2 finale, but that would have been pointless compared to everything else that was going on.
