I was able to steer the PCs away from a murderous path by establishing the dhampir as an ally who was able to communicate to the PCs that Siervage is a critical element in keeping the vampires from declaring open season on Caliphas. The PCs understood pretty well that the "right" thing to do was to support Siervage in maintaining order. Also, I played up Siervage's role in betraying the Tyrant at the end of the Shining Crusade (I think that's when it was), so the players (rightfully) viewed Siervage as an ally against the Whispering Way.
That was sufficient to keep down the murderousness once they got to the heart of the vampire underground. Of course, they got to kill many rebellious vampires on the way. I also felt it was necessary to make clear to the PCs that the vampire druid in the greenhouse was allied with Siervage's enemies, which is not the case in the module as written. It didn't seem to make sense to me that Siervage would be open to dealing with the PCs after they slaughtered the vampire druid. With my modification, that act actually did Siervage a favor.
So, you can steer the PCs without going as far as you are proposing, but I do think the idea of vampires seeking redemption is an interesting approach, and it seems fully consistent with the idea that Siervage is trying to find some space for vampire-human cohabitation. So, go for it!
As to your details, where is this clinic? I could imagine it being sort of at the sewer level, like a few other locations in the module. Or it could be a secret storefront at street level with access to the underground through a hole through which the vampires pass while gaseous (which is basically impossible for the PCs to find -- you don't really want them going underground just yet). I gather when the PCs go there, the clinic is empty? Any bodies? Any signs of struggle? Are they there with the authorities, or has someone else summoned the PCs and the PCs alone? Note that some of the details about HOW vampires are killed from the "Morning Murders" encounter is important, so I would perhaps include that. Maybe a vampire was captured and tossed into an alley and exposed to the morning sun?
I think your hints about the nature of the clinic are great and sufficient.
Regarding the business ledger, I wouldn't worry about it being too obvious, because the vampire connection in general will be obvious and come up soon in the module. The point of this is just to show another side to the vampires in a clever and cool way. But think carefully about WHEN you do it in terms of the direction of the adventure. And maybe it does not need to replace morning murders. Maybe it can be an additional encounter. Whatever seems best.
One suggestion: CHANGE THE PATIENT NAMES! This isn't the U.S. The names should have an Eastern European flavor. Just use a Hungarian name list or generator from Google!
The Owner's Journal seems great and certainly makes it clear the vampires are not uniformly murderous.
I might skip altogether on the survivor. It seems unnecessary and a bit heavy handed. If your players still want to kill all vampires after finding the other stuff, they are a lost cause. Maybe make it clearer by the records that the vampires are offering medical care. If you leave the survivor, then she becomes an NPC you will need to continue to use and perhaps become the main contact with the Underground. Maybe you want to do that, but I liked using the dhampir, who was in the middle rather than actually OF the vampire underground. One other point: I can't imagine the vampires wouldn't have exits in every room they could pass through in gaseous form, so it doesn't really make sense to me a survivor would be stuck hiding there...
Nice job with this!