What CTW Said Above
My immediate reaction to the OP was one of alarm. Indeed, distancing Folks from prior influences - not all of which statistically can be 'bad' - and putting in such long Work hours are tactics used by Scientology; the 'Moonies'; and a Group that tried to nab me once in San Francisco: 'Children Of God'. An alt explanation prior is that your BF's 'Inner Self' sensed, and feared, this over-control, and bolted from the Program before completion. Lawd knows I would have. From a pragmatic POV, where else now does he have to go?
While easier to say than do, you shouldn't beat yourself up over him not being the same, or breaking it off in Rehab. To gain small privileges, and move 'up' to other steps, appears to involve pleasing those in charge. Further, it sounds as if once he was trusted to regurgitate the Party Line, he was 'allowed' to tell you himself that he was done with you. His Handlers controlled the message to/from you. This is identical to mechanisms employed in Scientology.
You likely will find a very different Person returning to you. A subset of this very possibly will be that he's now sober and remains that way. However, so long a Program with such control factors in place will have molded him into what this Rehab Program expects, and creates in it's 'Graduates'. It will be inordinately painful for you, I'm guessing, to see these changes first hand and not be able to 'punch through' the Programming to the essential former Person. This same painfulness is a common experience for Relatives of Scientology Recruits where Alcohol/Drugs are not involved.
I'm an old dude. The details you outline, assuming they're accurate, lead to the outcome I'm suggesting. This sort of re-programming has been around for a very long time. I will accept that this sort of Rehab was '100% positive' in all aspects when you report back in and tell us so; regardless of your personal, Romantic interests. This sort of captive, long-term Rehab is what it takes for some Folks.
Frankly, you sound like a great and caring Gal whose 'mistake' is only that of following your Heart. Separating Financially and Legally [by rewriting your Will] is the easy part. Separating emotionally from a re-Programmed, vulnerable Person will be a rough ride, and I wish you well.
The Film 'Starman' is an interesting look at a Person who's not at all what he was before, and subsequently appears to be. It would be interesting for you to watch, and see what you might be in for.