To be fair to your husband I found through experience that the eldest usually gets the blame for things; other than that, him making unkind remarks to an impressionable teenager is unacceptable in my opinion. What your husband also doesn't realize is that he will turn the girls against his son if he's not carful, creating a pretty toxic environment in the process.
Since I have no children I can't say with any certainty that your husband should be able to love your two children as much as his own son, but preferential treatment is certainly unacceptable in my opinion.
As it stands I would regretfully say that I think you are already in damage control as far as this situation goes, your 16 year old daughter is vulnerable and impressionable and should be your priority right now. I think the best you can hope for is for your husband and daughter to just tolerate and accept each other. Your 16 year old is now acutely aware she has no father of her own, that your husband is not her father, and that she is only only one out of the three without a 'real' dad. This is not easy, and in my opinion your husband should know better than to make vitriolic comments to her. I can't blame the guy for snapping from time to time, none of us are perfect after all, but I'd say at the moment she needs to be the one you focus on. If for no other reason that the two others are impressionable and don't need to see all of the drama going on when they argue. I would work on strengthening the bond between the two of you, without making your 12 year old feel excluded and explain your intentions and reasoning to your husband. If he chooses not to listen then you need to prioritize and continue the mission alone. If things get too much can the 12 year old start spending more time with her dad whilst you work on this?